Example applications

Sorting an ensemble

The CREGEN routine that is used within the conformational search can also be used as an standalone tool. To use this you can simply call the routine by:

> crest struc.xyz -cregen ensemble.xyz

Here ensemble.xyz is the ensemble file that contains all the structures in the Xmol format.

Note

It is required to present a single reference structure (struc.xyz in the example above) of the molecule to check for CN clashes. Also, all structurues in the ensemble must have the same atom order.

Comparing two ensemble

Two ensembles generated on different levels of theory can be compared with the -compare option. Let’s assume that there are two ensembles v1.xyz, generated with the MF-MD-GC procedure and v2.xyz, generated with the default iMTD-GC workflow. To compare the 5 lowest conformers of each ensemble simply call:

> crest struc.xyz -compare v1.xyz v2.xyz -maxcomp 5

Which produces the output:

       ==============================================
       |                                            |
       |                 C R E S T                  |
       |                                            |
       |  Conformer-Rotamer Ensemble Sampling Tool  |
       |        based on the GFN-xTB method         |
       |             S.Grimme, P.Pracht             |
       |          Universitaet Bonn, MCTC           |
       ==============================================
       Version 2.7, Thu 27. Jun 13:41:37 CEST 2019
       Using the GFN-xTB code.
       Compatible with XTB version 6.1 and later.

 ---------------------
 Sorting file <v1.xyz>
 ---------------------
 running RMSDs... done.
  File <v1.xyz> contains 240 conformers.
  The 5 lowest conformers will be taken for the comparison:
  conformer  #rotamers
        1          1
        2          5
        3          3
        4          1
        5          2

 ---------------------
 Sorting file <v2.xyz>
 ---------------------
 running RMSDs... done.
  File <v2.xyz> contains 51 conformers.
  The 5 lowest conformers will be taken for the comparison:
  conformer  #rotamers
        1          6
        2          4
        3          3
        4          6
        5          4

 -----------------------
 Comparing the Ensembles
 -----------------------
 Calculating RMSDs between conformers... done.
 RMSD threshold:  0.1250 Å

 RMSD matrix:
  conformer          1          2          3          4          5
     1         0.01727    1.44147    1.56327    0.81845    0.83933
     2         0.00791    1.43084    1.56995    0.79512    0.83992
     3         1.43350    0.01254    0.80724    1.58138    1.59243
     4         0.12794    1.40597    1.54663    0.89315    0.83634
     5         0.14626    1.51398    1.56167    0.68473    0.88006

 --------------------------------
 Correlation between Conformers :
 --------------------------------
    #     Ensemble A             #    Ensemble B
                                 5     -33.87887
                                 4     -33.87937
                                 3     -33.87947
    5      -33.88008
    4      -33.88011
    3      -33.88017   <---->    2     -33.88016
    2      -33.88023   <---->    1     -33.88023
    1      -33.88023

 -----------------
 Wall Time Summary
 -----------------
--------------------
Overall wall time  : 0h : 0m : 0s

 CREST terminated normally.

From the output it can be seen that there is a correlation between the lowest conformers, i.e., the lowest conformers were found by both workflows. As the display options in the terminal are limited, an addtional file called rmsdmatch.dat is written, from which the exact correlation between the conformers of the two ensembles can be read. If, for example, two different levels of theory are used and the energies of the molecules in both ensembles are too different, then the output will not be of much use and one must refer to the rmsdmatch.dat file.

> cat rmsdmatch.dat
       1     1
       2     1
       3     2

Each line in this file consists of only two values a and b which denote that conformer a from ensemble A matches conformer b from ensemble B. In the example case shown above, the MF-MD-GC produced the lowest conformer twice, which both naturally match conformer 1 from the iMTD-GC procedure. The second conformer also is the same in both ensembles.

Note

In order for the comparison to work, both ensembles must have the same number of atoms with the same atom order in each structure. Furthermore the ensembles should be full CREs, i.e., rotamers should be present.

Constrained conformational sampling

Warning

The following application is still under development and should be considered an experimental feature.

It is possible to include additional constraints to all xtb calculations that are conducted by CREST. To do this one has to create a file called .constrains (or .xcontrol, both is valid) in the working directory, which contains the constraints in the exact same syntax as used by the xtb (see section Detailed Input) Constraints that are included via the .constrains file will be included in ALL calculations of the conformer search run. To circumvent name conventions a constrainement file under arbitrary name can directly be provided by the -cinp <FILE> option. Since this can overwrite settings created by CREST it should only be used very cautiously!

The main application for the additional constraints is the constrainment (fixing) of atoms, which could for example be used to sample only conformations for parts of a molecule. Another use could be the sampling of conformers for the transition state of an reaction.

To fix atoms it is also recommended to use an reference input file additionally to the normal structure input file, which is done with the argument reference=FILE in the .xcontrol file. Furthermore, fixed atoms should not be included in the RMSD of the MTD collective variables.

The content of the .xcontrol file for fixing atoms should look like the following example:

> cat .xcontrol
$constrain
  atoms: 4,8,10,12            # atoms 4, 8, 10 and 12 of some example molecule shall be constrained
  force constant=0.5
  reference=coord.original    # name of the reference file (just a copy of the input coord-file)
$metadyn
  atoms: 1-3,5-7,9,11         # atoms *included* to RMSD in the MTD (typically NOT the constrained atoms)
$end

This should ensure correct constrainment (as far as possible) in the MTD, as well as in the GFNn-xTB geometry optimization within a CREST run.

It is also possible to let CREST generate such a file automatically. To do this the list of atoms has to be provided with the flag --constrain <atom list>, i.e.,

> crest coord --constrain <atom list>

which will not start any calculation but instead write a file .xcontrol.sample that could subsequentially be used. Furthermore the file coord.ref will be created. (e.g. for a molecule with 65 atoms):

> crest coord --constrain 1,2,3,26-30

       ==============================================
       |                                            |
       |                 C R E S T                  |
       |                                            |
       |  Conformer-Rotamer Ensemble Sampling Tool  |
       |        based on the GFN-xTB method         |
       |             P.Pracht, S.Grimme             |
       |          Universitaet Bonn, MCTC           |
       ==============================================
       Version 2.8, Fri 25. Oct 12:04:52 CEST 2019
       Using the GFN-xTB code.
       Compatible with XTB version 6.1 and later.

 Command line input:
 > crest --constrain 1,2,3,26-30

 Input list of atoms: 1,2,3,26-30
 8 of 65 atoms will be constrained.
 A reference coord file coord.ref was created.
 The following will be written to <.xcontrol.sample>:

 > $constrain
 >   atoms: 1-3,26-30
 >   force constant=0.5
 >   reference=coord.ref
 > $metadyn
 >   atoms: 4-25,31-65
 > $end

<.xcontrol.sample> written. exit.

Note

Important: <atom list> must not contain any blanks and atoms must be seperated by comma. Ranges (e.g. 26-30) are allowed.

Sampling of noncovalent complexes and aggregates (NCI mode)

A specialized application of CREST is the sampling of aggregates (also refered to as NCI mode). The idea here is to find different conformations of non-covalently bound complexes in which the arrangement of the fragments is of interest. The application can be called by:

> crest struc.xyz -nci

The procedure and output is essentially the same as a normal iMTD-GC production run, but with reduced settings (less MTDs, different \(k\) and \(\alpha\)), and no genetic structure crossing. What is different, however, is that first a ellipsoide wall potential is created and added to the meta-dynamics. A nice example for this application are small molecular clusters, e.g. (H2O)6. The ellipsoide potential that is automatically determined for the input cluster is visualized in the figure below.

wclustpot

Visualization of an ellipsoide potential around (H2O)6 cluster.

The ellipsoide potential is required in the MTDs to counteract the bias potential, which would simply lead to a dissociation of the NCI complex after a few pico seconds (due to the maximization of the RMSD). In the subsequent geometry optimization, however, the surrounding potential must not be present since the bias potential is also not there and the structure would be artificially compressed by the ellipsoide. Hence it is automatically removed in the geometry optimizations

Note

The ellipsoide potential can be scaled by the factor REAL with the flag -wscal REAL.

Many new clusters are generated even for small NCI complexes, typically much more than conformers are generated for a single medium sized molecule. In general, the task of finding new low lying aggregates is much more challenging than finding (only) conformers, since each fragment of the complex could also have several different low lying conformations. For the (H2O)6 cluster 3 examples are shown in the figure below. Note that all three structures are also part of the well established WATER27 benchmark set, but were generated automatically by CREST from a single input structure. In total 69 different clusters were found of which only 3 are shown.

wclust1

Three automatically generated structures for a (H2O)6 cluster.

Molecular prototropy screening

Protonation site screening

The screening for possible protonation sites, i.e., for the different protomers of an molecule is possible by using a localized molecular orbital LMO approach. Herein, first the \(\pi\)- and LP-centers are determined by a GFNn-xTB calculation, and then all possible input structures are generated where a proton is placed at one of these centers. This procedure was first described in J. Comput. Chem., 2017, 38, 2618–2631.

The example calculation is performed for alanineglycine, in the gas phase, with the command

> crest struc.xyz -protonate

Which returns the following output:

       ==============================================
       |                                            |
       |                 C R E S T                  |
       |                                            |
       |  Conformer-Rotamer Ensemble Sampling Tool  |
       |        based on the GFN-xTB method         |
       |             S.Grimme, P.Pracht             |
       |          Universitaet Bonn, MCTC           |
       ==============================================
       Version 2.7.0, Mon 24. Jun 11:41:02 CEST 2019
       Using the GFN-xTB code.
       Compatible with XTB version 6.1 and later.

        __________________________________________
       |                                          |
       |       automated protonation script       |
       |__________________________________________|

 LMO calculation ... done.

-----------------------
Multilevel Optimization
-----------------------
 -------------------------
 1. crude pre-optimization
 -------------------------
 writing TMPCONF* Dirs from file "protonate_0.xyz" ... done.
 Starting optimization of generated structures
<.......>
 Now appending opt.xyz file with new structures
 12 structures remain within    90.00 kcal/mol window

 ---------------------
 2. loose optimization
 ---------------------
 writing TMPCONF* Dirs from file "protonate_1.xyz" ... done.
 Starting optimization of generated structures
<.......>
 Now appending opt.xyz file with new structures
 Structures sorted out due to dissociation:    1
 11 structures remain within    60.00 kcal/mol window

 --------------------------------------------
 3. optimization with user-defined thresholds
 --------------------------------------------
 writing TMPCONF* Dirs from file "protonate_2.xyz" ... done.
 Starting optimization of generated structures
<.......>
 Now appending opt.xyz file with new structures
 9 structures remain within    30.00 kcal/mol window

 ===================================================
 Identifying topologically equivalent structures:
 Equivalent to 1. structure: 2 structure(s).
 Equivalent to 3. structure: 5 structure(s).
 Equivalent to 5. structure: 2 structure(s).
 Done.
 Appending file <protonated.xyz> with structures.

 Initial 9 structures from file protonate_3.xyz have
 been reduced to 3 topologically unique structures.

===================================================
============= ordered structure list ==============
===================================================
 written to file <protonated.xyz>

 structure    ΔE(kcal/mol)   Etot(Eh)
    1            0.00        -33.964453
    2            3.51        -33.958853
    3            5.75        -33.955296


 -----------------
 Wall Time Summary
 -----------------
           LMO calc. wall time :         0h : 0m : 0s
      multilevel OPT wall time :         0h : 0m : 3s
--------------------
Overall wall time  : 0h : 0m : 4s

 CREST terminated normally.

As one can see from the output, three possible protomers of alanineglycine were found at the GFN2-xTB level (within the default 30 kcal/mol energy window around the most stable protomer). This ensemble of structures is written to a file called protomers.xyz. The first (lowest) protomer created by CREST for this molecule includes a ring-closure, apparently caused by the addition of the proton. This nicely demonstrates the ability of our approach to form and break new bonds. The three protomers are shown in the figure below.

alaglyprot

Three lowest protomers of alanineglycine generated by CREST at the GFN2-xTB level.

Deprotonation site screening

The general approach to find deprotonation sites at a GFN level is much more simple than finding protonation sites. For each hydrogen atom in the structure a new (deprotonated) reference structure is created and optimized in a multilevel approach. The commandline argument to invoke this search is:

> crest struc.xyz -deprotonate

For the example of alanineglycine, again three structures are obtained and written to a file called deprotonated.xyz:

<.......>
<.......>

===================================================
============= ordered structure list ==============
===================================================
 written to file <deprotonated.xyz>

 structure    ΔE(kcal/mol)   Etot(Eh)
    1            0.00        -33.593702
    2           21.83        -33.558913
    3           25.12        -33.553669

<.......>
<.......>

However, two of the three structures have much higher energies and therefore mainly the lowest deprotomer should be considered.

alaglydeprot

Lowest deprotomer of alanineglycine at the GFN2-xTB level. The deprotonation happens at the carboxyl group.

Tautomerization screening

The last application of the different prototropy screening protocols is an automatized tautomerization tool, which utilizes both the protonation and deprotonation procedures presented in the previous two subsections. By first protonating a molecule and then deprotonation of the resulting protomers at all postions, prototropic tautomers relative to the initial input structure can be found. A single cycle of this protonation/deprotonation in principle yields all tautomers with a single hydrogen permutation relative to the input. If a higher number of hydrogen permutations is required, the procedure can simply be repeated with the created tautomers, i.e., tautomers with two or more hydrogen atom permutations are generated. From experience, however, it is generally sufficient to repeat this protonation/deprotonation cycle twice (which is the default in CREST), in order to get the relevant low energy tautomers. The approach was first described in J. Comput.-Aided Mol. Des., 2018, 32, 1139-1149. The tautomerization search can be conducted by the command

> crest struc.xyz -tautomerize

Tip

The number of protonation/deprotonation cycles can be adjustet with the flag -iter INT, where INT is the number of cycles.

For alanineglycine the following output is generated:

       ==============================================
       |                                            |
       |                 C R E S T                  |
       |                                            |
       |  Conformer-Rotamer Ensemble Sampling Tool  |
       |        based on the GFN-xTB method         |
       |             S.Grimme, P.Pracht             |
       |          Universitaet Bonn, MCTC           |
       ==============================================
       Version 2.7.0, Mon 24. Jun 11:41:02 CEST 2019
       Using the GFN-xTB code.
       Compatible with XTB version 6.1 and later.

        __________________________________________
       |                                          |
       |     automated tautomerization script     |
       |__________________________________________|

*******************************************************************************************
**                   P R O T O N A T I O N   C Y C L E     1 of 2                        **
*******************************************************************************************

 LMO calculation ... done.
-----------------------
Multilevel Optimization
-----------------------
<.......>
 ===================================================
 Identifying topologically equivalent structures:
<.......>
 Appending file <protonated.xyz> with structures.

 Initial 9 structures from file protonate_2.xyz have
 been reduced to 3 topologically unique structures.
 ===================================================
 ============= ordered structure list ==============
 ===================================================
 written to file <protonated.xyz>

 structure    ΔE(kcal/mol)   Etot(Eh)
    1            0.00        -33.964400
    2            3.60        -33.958659
    3            5.78        -33.955188

*******************************************************************************************
**                 D E P R O T O N A T I O N   C Y C L E     1 of 2                      **
*******************************************************************************************
-----------------------
Multilevel Optimization
-----------------------
<.......>
 ===================================================
 Identifying topologically equivalent structures:
<.......>
 Appending file <deprotonated.xyz> with structures.

 Initial 24 structures from file deprotonate_2.xyz have
 been reduced to 8 topologically unique structures.
 ===================================================
 ============= ordered structure list ==============
 ===================================================
 written to file <deprotonated.xyz>

 structure    ΔE(kcal/mol)   Etot(Eh)
<.......>

*******************************************************************************************
**                   P R O T O N A T I O N   C Y C L E     2 of 2                        **
*******************************************************************************************
Calculating LMOs for all structures in file <tautomerize_1.xyz>
<.......>
Collecting generated protomers ... done.

-----------------------
Multilevel Optimization
-----------------------
<.......>
 ===================================================
 Identifying topologically equivalent structures:
<.......>
 Appending file <protonated.xyz> with structures.

 Initial 51 structures from file protonate_1.xyz have
 been reduced to 17 topologically unique structures.
 ===================================================
 ============= ordered structure list ==============
 ===================================================
 written to file <protonated.xyz>

 structure    ΔE(kcal/mol)   Etot(Eh)
<.......>

*******************************************************************************************
**                 D E P R O T O N A T I O N   C Y C L E     2 of 2                      **
*******************************************************************************************
-----------------------
Multilevel Optimization
-----------------------
<.......>
 ===================================================
 Identifying topologically equivalent structures:
<.......>
 Appending file <deprotonated.xyz> with structures.

 Initial 95 structures from file deprotonate_2.xyz have
 been reduced to 19 topologically unique structures.
 ===================================================
 ============= ordered structure list ==============
 ===================================================
 written to file <deprotonated.xyz>

 structure    ΔE(kcal/mol)   Etot(Eh)
<.......>

*******************************************************************************************
**                               T A U T O M E R I Z E                                   **
*******************************************************************************************
 ---------------------------
 Final Geometry Optimization
 ---------------------------
<.......>
 ===================================================
 Identifying topologically equivalent structures:
 Done.
 Appending file <tautomers.xyz> with structures.

 All initial 19 structures from file tautomerize_4.xyz are unique.

===================================================
============= ordered structure list ==============
===================================================
 written to file <tautomers.xyz>

 structure    ΔE(kcal/mol)   Etot(Eh)
    1            0.00        -33.867777
    2            1.99        -33.864606
    3            3.84        -33.861657
    4            3.84        -33.861656
    5            4.42        -33.860731
    6            4.68        -33.860314
    7           10.63        -33.850839
    8           10.79        -33.850575
    9           10.92        -33.850381
   10           10.95        -33.850329
   11           12.18        -33.848371
   12           12.18        -33.848371
   13           13.45        -33.846343
   14           19.21        -33.837164
   15           19.21        -33.837164
   16           20.24        -33.835520
   17           24.97        -33.827984
   18           25.58        -33.827014
   19           29.53        -33.820725


 -----------------
 Wall Time Summary
 -----------------
           LMO calc. wall time :         0h : 0m : 0s
      multilevel OPT wall time :         0h : 0m :31s
--------------------
Overall wall time  : 0h : 0m :32s

 CREST terminated normally.

As can be seen from the output, the entire procedure is constructed from the protonation and deprotonation site screening routines. The first protonation step yields the same three protomers that are also obtained by the standalone application, which are then automatically deprotonated. Two protonation/deprotonation cycles are performed. The final tautomer ensemble consists of 19 structures (within 30 kcal/mol) and is written to the file tautomers.xyz.

Property calculations on final ensemble

It is possible to (automatically) perform further calculations on the final conformer ensemble by the usage of the -prop option:

> crest [input] [options] -prop [property option]

Currently there are only some few options available but we plan to implement more.

A useful type of this mode, e.g. is the the reoptimization of the conformer ensemble with very tight convergence thresholds. In combination with crude conformational search settings such as -qucik, -squick or -mquick this helps to ensure the ensemble convergence, i.e., the minimization of artificial structural differences for the same conformer due to too loose geometry optimizations. This reoptimization can be requested by

> crest coord -mquick -prop reopt

Updated geometries will generally be written to a new ensemble file called crest_property.xyz.

Another useful runtype of this mode is the calculation of frequencies and reweighting of the conformers on the resulting free energies. E.g.:

> crest coord -prop hess

The property mode can also directly be applied to a given ensemble:

> crest -forall <ensemble>.xyz -prop [property option]

Dry run to check settings prior to calculations

A dry run can be performed by CREST to verify the settings that would be applied in the calculation. To do this, simply add the -dry flag to the cmd-input line.

> crest [input] [options] -dry

Whit this option nothing will be actually be calculated but instead the settings are printed. E.g. for some random setting:

> crest coord -ewin 3.2 -temp 999 -gfn1 -nozs -chrg 1 -cinp .xcontrol.sample -dry

<....>
<....>
*******************************************************************************************
**                                  D R Y    R U N                                       **
*******************************************************************************************
 Dry run was requested.
 Running CREST with the chosen cmd arguments will result in the following settings:

 Input file : coord

 Job type :
  1.  Conformational search via the iMTD-GC algo

 Job settings
  sort Z-matrix        :      F

 CRE settings
  energy window         (-ewin) :    3.2000
  RMSD threshold        (-rthr) :    0.1250
  energy threshold      (-ethr) :    0.1000
  rot. const. threshold (-bthr) :    0.0200
  T (for boltz. weight) (-temp) :    999.00

 General MD/MTD settings
  simulation length [ps]    (-len) : <system dependent>
  time step [fs]          (-tstep) :       5.0
  shake mode              (-shake) :         2
  MTD temperature [K]    (-mdtemp) :    300.00
  trj dump step  [fs]    (-mddump) :       100
  MTD Vbias dump [ps]    (-vbdump) :       1.0

 Constrainment info
  applying constraints?  :       T
  constraining file      : .xcontrol.sample
  file content :
  > $constrain
  >   atoms: 1-3,26-30
  >   force constant=0.5
  >   reference=coord.ref
  > $metadyn
  >   atoms: 4-25,31-65
  > $end

 XTB settings
  binary name        (-xnam) : xtb
  GFN method         (-gfn)  : --gfn1
  (final) opt level  (-opt)  : 2
  Molecular charge   (-chrg) : 1

 Technical settings
  working directory : /home/philipp/calculations/cresttest
  CPUs (threads)     (-T) : 4


normal dry run termination.

Examples from the paper: Automated exploration of the low-energy chemical space with fast quantum chemical methods

Conformers of transition-states

At first a transition-state (TS) has to be localized. Then the TS mode has to be identified and reasonable constrains have to be applied to freeze this mode during the CREST run. Choosing suitable constrains is the responsibility of the user.

TS COMT

Tranisition state of the active site of the COMT enzyme. TS mode highlighted in blue. (Mg2+ in green, sulfur in yellow).

In this example a methyl group is transfered onto the catechol molecule.

cat coord.ref
$coord
    -2.57480197685137   -0.38573933229522    0.86228536590435      Mg
    -5.87996595426622   -1.46598597135567   -1.00931632324148      O
    -5.79755045954234    1.88737481602186    1.36486580018227      O
    -6.93504356011937    0.41703174067196   -0.07677235660280      C
    -9.68583177367761    0.93957235453071   -0.70260934507636      C
    -9.88785370898918    2.90051382662291   -1.27585066001173      H
    -10.31204304615949  -0.31693795001232   -2.19707799857187      H
    -10.81224558069477   0.63532604630470    0.98871505743889      H
    -1.35732893615725    2.84149984259631    3.74273757259152      O
    -1.31788637685368    1.88478932440519   -1.80336662588251      O
    -1.03506712269361   -3.09136305475668   -1.65209468828016      O
    -3.01034174150676    3.35231258504990    4.30691490291278      H
    -0.64007292100150    4.31049584542225    2.93186531615926      H
    -3.02042382593105   -2.69109360436689    3.78441246580865      O
    -0.67413309122153   -2.78784634989936    4.10013037720282      C
     0.80704125300360   -1.59087682326574    2.72475235410942      O
     0.37030033373577   -4.45667671167827    6.17913372417457      C
     1.65729077111170   -3.36053569450090    7.34278701173010      H
    -1.17079464125707   -5.18933342363882    7.31676317209597      H
     1.41212360996512   -6.00880794547076    5.32805483610633      H
    -0.04610218809699    0.99217247488345   -2.84947633284740      H
    -0.58166801572397    4.35407649708453   -2.13719082516246      C
     1.69930763718877    4.60968100984284   -3.53188509022323      C
    -1.89895861199073    6.41295502711680   -1.26089925937752      C
     2.61815567802848    7.04758861150735   -3.94211016089909      C
    -0.94293511850593    8.82264113991643   -1.71734825726509      C
    -3.65794447068903    6.13213826999732   -0.25859371242962      H
     1.29133066638906    9.11831895867148   -3.04019344765619      C
     4.35136261809131    7.29515670682662   -4.99253235854911      H
    -1.96139641783255   10.45433175989920   -1.03894063047482      H
     2.01793975704253   10.99527109251927   -3.38477251662235      H
     5.63677744964081   -0.19526366812337   -3.54734464996746      H
     3.55857435122244    0.44545364581733   -0.79647639427433      H
     6.02794370271953    2.75567866080431   -1.74563412676399      H
     2.74773927853638    2.50310064429053   -4.32763740793204      O
     5.16232303152189    0.93488296527549   -1.93713143185301      C
     7.77908129622702   -0.95480533027442    0.60724611364076      S
     6.20470140355368   -3.99408071134196    0.68137239550646      C
     7.00770708640275   -5.10883646299712    2.20213746286551      H
     4.19551348270129   -3.68373090740626    0.97362752914345      H
     6.54643468112530   -4.90904155689111   -1.11917138292065      H
     6.61325357496481    0.34737209228094    3.55003016825311      C
     7.52593267335208   -0.62757026577676    5.10500275305939      H
     7.10342021330197    2.33658535430792    3.58672294810726      H
     4.57513571292400    0.10172782556556    3.62256009227771      H
    -1.61022171124489   -5.31411191371024   -2.02789529853598      C
    -3.17527947979499   -6.57718946281529   -0.51674594958634      N
    -3.77763814894346   -8.33207207055257   -0.93763600526181      H
    -4.05833804986482   -5.57635320116590    0.85099090510650      H
    -0.47266612030322   -6.78426594278943   -4.18601622917577      C
     0.51805850799787   -8.43374379675092   -3.46937160488911      H
    -1.96305386150678   -7.41025810365247   -5.45278966275112      H
     0.83013814067146   -5.58152886274452   -5.21822759129119      H
$end

To preserve the TS vibrational mode the atoms which are dominantly contributing to this mode are fixed. In this case the carbon (36) of the methyl group being transferred, the sulfur (37) of the S-adenosyl- L -methionine (SAM) and the oxygen (35) of the catechol group are constrained. For running the TS conformational search only these atoms have to be constrained. But to retain the surrounding enzyme environment additionally the distances of all ligands to the magnesium cation and the amide magnesium water angle were constrained. As stated before all atoms with constrains have to be removed from the list of atoms which are used in the metadynamics simulation.

$constrain
atoms: 35-37
force constant=0.5
reference=coord.ref
distance: 10, 1, auto
distance: 2, 1, auto
distance: 11, 1, auto
distance: 14, 1, auto
distance: 9, 1, auto
angle: 9, 1, 11, 180
$metadyn
atoms: 3-8,12-13,15-34,38-53
$end
crest coord -cinp .constraintinp -g methanol > crest.out

The TS conformer search yields 141 conformers within 6 kcal/mol. On these conformers hessians have to be calculated to ensure that the transition-state mode is preserved. Those conformers with preserved mode can be optimized into the TS and the true TSs have to be confirmed by again a hessian calculation (only one imaginary mode). During the optimization some conformers can become identical or rotamers of each other. To this end all optimized geometries are appended and sorted with the cregen sorting routine.

cat TSconf*.xyz >> allts.xyz

crest coord -cregen allts.xyz -ewin 30 > sorting.out
TS COMT conformers

Tranisition state conformers of the active site of the COMT enzyme. (Mg2+ in green, sulfur in yellow, water oxygen in blue). Hydrogen atoms are omitted for clarity.

Now after sorting only 91 unique TS conformers are optained within an energy window of 6.1 kcal/mol. This procedure can in principle be refinded at DFT level.

Conformers of metal-organic systems

  • trans-Cu(II)(L-valine)2

Calculation of trans-Cu(II)(L-valine)2 conformers in the gas phase.

`trans`-Cu(II)(L-valine)2
cat coord

$coord
 -0.002022192318         -0.000684522852          1.349121896005     CU
  2.028671941135          2.818125977315          1.174767316951     O
  4.406562542342          2.529552834523          0.838287117696     C
  5.900488893190          4.242544277537          0.591753944418     O
  5.382406579092         -0.254197829091          0.699650595616     C
  3.456927714843         -1.958681435237          1.737975874213     N
  3.442953703137         -3.661542617496          0.846227450863     H
  3.710547158869         -2.249430796311          3.618554595139     H
  7.133224715719         -0.349791899055          1.804782999185     H
  6.007018333138         -0.877714812490         -2.069473442827     C
  7.266213509953         -3.466799912264         -2.312238367182     C
  8.881995597301         -3.618089140164         -1.050454618739     H
  7.930334466002         -3.738254167109         -4.236839656939     H
  5.952357752542         -4.994107920656         -1.890594175637     H
  3.663534173447         -0.712885768717         -3.746419767180     C
  4.156219468360         -1.164942859389         -5.689573088070     H
  2.890265219159          1.189883399588         -3.704912704715     H
  2.203522204085         -2.025873622846         -3.126878925482     H
  7.355957431563          0.567207315613         -2.680683804317     H
 -2.033163868813         -2.819780021566          1.179505209377     O
 -4.409877555278         -2.530551975348          0.835068556898     C
 -5.903043316660         -4.243023566156          0.580387940800     O
 -5.384798675016          0.253509426488          0.697143335052     C
 -3.461334991004          1.955672873602          1.742931448447     N
 -3.448757571238          3.662158486139          0.858135081470     H
 -3.716247763220          2.238184300034          3.624611253622     H
 -7.138671974341          0.348502264395          1.797538738740     H
 -6.001307995929          0.880859137312         -2.072901114603     C
 -7.255902292489          3.472119634743         -2.316426880308     C
 -7.917767124579          3.744910887179         -4.241612390481     H
 -5.939710712311          4.997073845686         -1.893506102537     H
 -8.872648523224          3.626011270865         -1.056195385178     H
 -3.653380600330          0.714736239795         -3.743504646086     C
 -2.884657484645         -1.189944325855         -3.704494974332     H
 -2.192229886598          2.022965931298         -3.116395721134     H
 -4.139423979729          1.172691111744         -5.686934420106     H
 -7.350580840264         -0.561585906341         -2.689213500551     H
$end

crest coord -nci > crest.out

Results in 28 conformers within an energy window of 6 kcal/mol.

  • [Pt(COMe)2(2-py)3COH] conformers in methanol.
[Pt(COMe)2(2-py)3COH] in methanol
cat coord
$coord
    1.48235976014562      0.32575477023909      0.83983586742930      pt
    4.37233116325056     -2.04701937728251      0.66066526359202       c
    5.11582123352082     -2.89977152283009     -1.35531347223172       o
    5.60331010456907     -2.97886601012202      3.10440618630801       c
    5.11582123352082     -1.79782119213888      4.71363082065877       h
    4.96457322302306     -4.90914755554552      3.43123243126445       h
    7.64542186308448     -3.03767428737742      2.85382472163511       h
    3.90413261656682      3.15849014823120      0.32067896584616       c
    3.77547628198769      4.50973504009881     -1.55263489557537       o
    5.78086877201500      3.82467530185737      2.40255812110202       c
    6.44902868945004      5.75938447561023      2.16769917785472       h
    4.93481948506077      3.56859662386391      4.26032709535443       h
    7.38167845589603      2.54234683232997      2.24297074917982       h
   -1.45880054444693     -2.37015120764916      1.99982157738756       n
   -1.37380633216814     -3.71993156176379      4.12084829921227       c
   -3.47313332880892     -4.91477704969539      5.12088380983082       c
   -5.76730431783315     -4.67836853101913      3.87619679514437       c
   -5.86160354159028     -3.26072055256804      1.67926544374004       c
   -3.65812239940936     -2.14869231241016      0.79621720883004       c
   -3.66283159693252     -0.54983471562441     -1.60480456492594       c
   -1.36490194262998     -1.28858913220566     -3.20027766220770       c
   -1.32606807059918     -3.74293708770554     -3.74494019740640       n
    0.45445456851927     -4.60152659727760     -5.28248940926294       c
    2.25936790283487     -3.06404352583571     -6.38168829870466       c
    2.17878809080250     -0.49502320914006     -5.86813254537940       c
    0.32467195716495      0.43733364975533     -4.26146660021256       c
    0.14833216307473      2.45190076015779     -3.96574713712955       h
    3.52744783732032      0.78490530819858     -6.70693851206628       h
    3.68438581320421     -3.84772429150018     -7.60737222739882       h
    0.39857914622211     -6.61487483432435     -5.63264243360372       h
   -5.86517134452916     -0.98949461824931     -3.04219073283502       o
   -5.69660399402350     -2.62769064394335     -3.83817172589844       h
   -3.63492223167593      2.20020246734036     -0.78356738209650       c
   -1.79344269668899      2.91320936536104      0.78584828153889       n
   -1.75920841806563      5.28509912105245      1.61658700736449       c
   -3.54797404257573      7.05739011313605      0.91252418313075       c
   -5.45207721188036      6.32967358689699     -0.73330822586627       c
   -5.50553000527517      3.85501674464698     -1.58299523562631       c
   -6.94955289136293      3.18275045232518     -2.84989409127871       h
   -6.87435123990475      7.65734792470912     -1.34159783995923       h
   -3.43966438926938      8.95769115346132      1.63587922145511       h
   -0.24274666012596      5.76489302728759      2.90140613593504       h
   -7.59878342212486     -2.99720202278941      0.64743151148342       h
   -7.44966324325272     -5.57429713925087      4.59918333687282       h
   -3.30863455866736     -5.99888080678762      6.83682316863177       h
    0.45096235462570     -3.84321729467325      5.03295296314152       h
$end

crest coord -g methanol -ewin 10 > crest.out

The search for the Pt-complex conformers results in 68 conformers within an energy window of 10 kcal/mol.

Conformational search of tyrosine on a graphene surface

To sample a tyrosine molecule at a graphene surface, the graphene sheet has to be constrained. All atoms in the graphene layer are constrained and removed from the metadynamics list.

tyrosine on graphene surface
cat .constrains

$constrain
    atoms: 1-252
    force constant=0.5
    reference=coord.input-original
    $metadyn
    atoms: 253-276
$end

cat coord.input-original

$coord
    25.57030991921202   -1.29059115296523   -0.00598160501741      C
    25.57044241258889    1.28341269512943   -0.00397025649369      C
    23.26056590790795    2.70217665940709   -0.00029100251731      C
    23.24029402398585    5.32779404644931    0.00100734191172      C
    20.94157103860908    6.71653777403401    0.00350095166658      C
    20.91152361664611    9.36664222799565    0.00390218154564      C
    18.62125921494789   10.73533662251798    0.00644642379287      C
    18.58134086796354   13.40310199790359    0.00577252431633      C
    16.30144187186615   14.75441822463413    0.00911453357094      C
    16.24838174294015   17.43954219647988    0.00645557179198      C
    13.98481323267349   18.77014376357869    0.00996412506652      C
    13.91132086532623   21.47993962309619    0.00398308521361      C
    11.68223395792687   22.76705405593083    0.00667868517840      C
    23.23975279130400   -5.33474095446540   -0.00731302769541      C
    23.26029458648507   -2.70912180306862   -0.00467349937707      C
    20.93174016704535   -1.33727196043975   -0.00133108922934      C
    20.93188342707722    1.33055529046503    0.00081585427198      C
    18.61221093462830    2.68271748197896    0.00282646704916      C
    18.60800793365893    5.36022077189572    0.00464910445605      C
    16.29058723267624    6.70694827919018    0.00657403025646      C
    16.28436011426403    9.38628406493185    0.00875170443409      C
    13.96723583506467   10.73158318782874    0.01208246556117      C
    13.95992943220878   13.41187709257133    0.01391081920492      C
    11.64338138388279   14.75451471117306    0.01811199832376      C
    11.63248103339880   17.43948496412882    0.01741770073639      C
    9.32215273401024    18.77351998648383    0.02061202665840      C
    9.29861569072829    21.47602775444658    0.01579094470882      C
    7.01463133268908    22.77127484019967    0.01713945360400      C
    20.91057452024432   -9.37335860619177   -0.00926090528278      C
    20.94088299656363   -6.72324817926078   -0.00658702044546      C
    18.60745075594095   -5.36670680488450   -0.00374295822885      C
    18.61193643260484   -2.68920008796749   -0.00153341601501      C
    16.28742192884590   -1.34235637938395   -0.00078002692156      C
    16.28757499289433    1.33609346344897    0.00147976178734      C
    13.96434116375503    2.68237236768262    0.00076404228717      C
    13.96287174466134    5.36168711625019    0.00444321914007      C
    11.64121337713845    6.70589478724923    0.00506279531532      C
    11.63822495880011    9.38856356746231    0.01140806380708      C
    9.31876144361668    10.72973740054357    0.01538062834809      C
    9.31472052037413    13.41484574971875    0.02046267069700      C
    6.99521035114103    14.75419616780989    0.02462006312471      C
    6.99130768004798    17.44070137881147    0.02532754092530      C
    4.67042012951467    18.77581140475820    0.02736696446206      C
    4.66258399962784    21.47489924179938    0.02293852266839      C
    2.35249685077769    22.77391798267787    0.02212621551956      C
    18.57998109654765  -13.40958568048023   -0.01028264322867      C
    18.62015473984217  -10.74181472085148   -0.00815563904508      C
    16.28339497432454   -9.39252741923171   -0.00521520823422      C
    16.28988963380622   -6.71318737538808   -0.00404056626572      C
    13.96230713311354   -5.36770826591533   -0.00442097129394      C
    13.96405926362842   -2.68839552363364   -0.00377125200632      C
    11.63966160646814   -1.34407984382584   -0.00904818073003      C
    11.63980125609782    1.33828860894632   -0.00694514984261      C
    9.31718204611965     2.68076977770467   -0.01577395709023      C
    9.31651311270946     5.36383477266664   -0.00518866604770      C
    6.99345645543046     6.70626536261829   -0.00580602080543      C
    6.99238975005242     9.38889650419404    0.01018123529597      C
    4.66942445816832    10.73022469984729    0.01596892428477      C
    4.66767523754332    13.41536689488851    0.02498093342981      C
    2.34659451442003    14.75374729750557    0.02932151339149      C
    2.34541319267838    17.44224899252958    0.03052836779358      C
    0.02192747834666    18.77650769724976    0.03128547441315      C
    0.02204581702233    21.47485010389652    0.02595882570531      C
    -2.30827777761409   22.77415959011223    0.02256838460730      C
    16.24661075554111  -17.44578823181741   -0.01013734215265      C
    16.29993060120758  -14.76066846818401   -0.00812704005076      C
    13.95855696550417  -13.41788125850394   -0.00444039516866      C
    13.96612442985704  -10.73758744438051   -0.00414530231920      C
    11.63725550740641   -9.39433325364823   -0.00401359135821      C
    11.64051700131476   -6.71165587242432   -0.00602746222362      C
    9.31595899918277    -5.36940309841218   -0.01310009453262      C
    9.31693993550326    -2.68633606543353   -0.01891241488459      C
    6.99250858337540    -1.34364841298911   -0.04053087185396      C
    6.99262614528279     1.33843607842166   -0.04039634224145      C
    4.66829807447026     2.68060255606494   -0.05849331187865      C
    4.66838077810071     5.36444295219266   -0.02946711255395      C
    2.34546795808210     6.70546777798594   -0.02011056812930      C
    2.34548672067421     9.39005944206936    0.00792927448916      C
    0.02151160692621    10.73096229461900    0.01836028425584      C
    0.02166355850542    13.41525943333584    0.02919214654642      C
    -2.30314738868724   14.75399842979222    0.03371873327606      C
    -2.30170671357899   17.44247566484074    0.03391819200193      C
    -4.62657873721502   18.77628435247385    0.03298595758151      C
    -4.61848784408495   21.47537522910175    0.02560169171120      C
    -6.97041113719043   22.77198785523224    0.01911534529519      C
    13.90914113254730  -21.48594598108393   -0.01033584558689      C
    13.98290020369888  -18.77616131023010   -0.00756967293109      C
    11.63069926259142  -17.44525404116543   -0.00301796684893      C
    11.64186594877656  -14.76028958926714   -0.00225240122053      C
    9.31334018064636   -13.42037835388799   -0.00050064690806      C
    9.31765144447383   -10.73527777129347   -0.00273906743608      C
    6.99141240533732    -9.39419601810598   -0.00610150867183      C
    6.99273536257410    -6.71153949160536   -0.01572184076338      C
    4.66777019559512    -5.36946863827436   -0.03472958133329      C
    4.66784980463537    -2.68568430403884   -0.05767595376480      C
    2.34451914565195    -1.34413003433670   -0.08972846459708      C
    2.34456672574876     1.33936603534043   -0.08992506624553      C
    0.02090811162037     2.68094549890774   -0.08525730399650      C
    0.02111281557256     5.36367785785738   -0.04218166058112      C
    -2.30319003521588    6.70557418244421   -0.01593859385830      C
    -2.30260481415700    9.39011489524983    0.01310861544943      C
    -4.62640274973063   10.73069866586899    0.02658914458233      C
    -4.62436575510021   13.41584995240830    0.03462561586354      C
    -6.95176077190229   14.75491657239231    0.03775667851738      C
    -6.94759324240958   17.44141219089441    0.03541282761784      C
    -9.27832130444150   18.77446705578989    0.03155385525560      C
    -9.25452218190166   21.47696510552652    0.02154959462713      C
    -11.63802237495646  22.76822838541283    0.01080138060727      C
    11.67992598947008  -22.77283570051328   -0.00834317870550      C
    9.29642984746100   -21.48156460163871   -0.00342311682088      C
    9.32023206578185   -18.77906553363732   -0.00092512411397      C
    6.98952062190846   -17.44599854678769    0.00224945815385      C
    6.99369455574676   -14.75950793677676    0.00199456075935      C
    4.66628544326049   -13.42042472957629    0.00282443615400      C
    4.66831941671158   -10.73531049956183   -0.00294605654817      C
    2.34450022003777    -9.39484861167554   -0.00889347428569      C
    2.34477736575761    -6.71029850254746   -0.03096748479269      C
    0.02065664441757    -5.36823814102908   -0.05222779425988      C
    0.02061674289975    -2.68553888940278   -0.08961100122795      C
    -2.30299554292030   -1.34344598487105   -0.09950976794014      C
    -2.30319722664585    1.33939473396005   -0.09532505353303      C
    -4.62645210980409    2.68061978914947   -0.05798804837452      C
    -4.62592518953837    5.36451283149119   -0.02208304225800      C
    -6.95072782946171    6.70669485989158    0.00967601306812      C
    -6.94947330532319    9.38953936851952    0.02696512792323      C
    -9.27574242491885   10.73068901863044    0.03718718622128      C
    -9.27141379657199   13.41578622554120    0.03931193737819      C
    -11.59995375468507  14.75568934423370    0.03834655662908      C
    -11.58877757429171  17.44065888647631    0.03293785817032      C
    -13.94098976946021  18.77156069186492    0.02430444214536      C
    -13.86724120028323  21.48133630468718    0.01214297052796      C
    7.01231720722008   -22.77658999388850   -0.00234006341816      C
    4.66040268911371   -21.47996607848377    0.00149181176170      C
    4.66849920833472   -18.78088401746963    0.00410568098744      C
    2.34362579491293   -17.44706779691327    0.00732146583161      C
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    -4.62622443840555   -5.36874676215761   -0.03339361896089      C
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    -18.56551946921603   5.36209334622057    0.04362492655707      C
    -20.89893941447967   6.71862640748693    0.03789971221054      C
    -20.86865960792762   9.36876159820730    0.03406103920853      C
    -6.97271504105007  -22.77586361153682    0.00935838286716      C
    -9.25669092524713  -21.48062873166514    0.01464909085110      C
    -9.28021281259710  -18.77810879610820    0.02202485039542      C
    -11.59052242604395 -17.44410052767191    0.02647854971243      C
    -11.60145002198461 -14.75911576806898    0.03137927696694      C
    -13.91795480666969 -13.41649851415307    0.03453120183778      C
    -13.92534496735509 -10.73623164754813    0.03777440130243      C
    -16.24240899490235  -9.39087823040052    0.03971902111664      C
    -16.24866335594347  -6.71158439878077    0.04219316440738      C
    -18.56607436613115  -5.36482318773708    0.04295591350027      C
    -18.57022407662064  -2.68731099765057    0.04509190423409      C
    -20.88994797246661  -1.33517424888670    0.04277804898084      C
    -20.88978625036696   1.33266943321888    0.04291787852488      C
    -23.21836627451592   2.70450487214013    0.03585894903904      C
    -23.19782862886721   5.33013495599820    0.03371371345388      C
    -11.64032273972809 -22.77163940053880    0.01115915464150      C
    -13.86940415391146 -21.48452960645214    0.01502776534082      C
    -13.94287827178937 -18.77473621915132    0.02304401301909      C
    -16.20643726826264 -17.44413581852868    0.02513847957228      C
    -16.25951045997595 -14.75902200044161    0.03084954628687      C
    -18.53937846949824 -13.40770271952225    0.03099249125201      C
    -18.57933718203032 -10.73994015797348    0.03538752690595      C
    -20.86957513685626  -9.37125530274323    0.03362309165171      C
    -20.89962154329600  -6.72113971988435    0.03730374506769      C
    -23.19836258846670  -5.33240814471403    0.03315712568452      C
    -23.21862068513432  -2.70678194350826    0.03552676773095      C
    -25.52851798119108  -1.28802447569940    0.02763182281201      C
    -25.52838492985103   1.28598364520524    0.02783532490532      C
    -11.59074743477874  24.77707891388043   -0.00207055884898      H
    -15.63049848787903  22.44499757871727    0.00040984411316      H
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    6.98981614929314    24.77638545989041    0.01047133295866      H
    11.63514864567720   24.77592617817733   -0.00059419108331      H
    15.67467228639966   22.44343307339889   -0.00554839493035      H
    17.99735162326968   18.42044292331396   -0.00133080202233      H
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    24.96436574768334    6.35183557721443   -0.00080698816161      H
    27.28664220260683    2.32861760145338   -0.00578136872665      H
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    15.67240208823021  -22.44961809552324   -0.01504494465218      H
    11.63264076908928  -24.78170207940770   -0.01131205807999      H
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    -27.24448188791929   2.33134552584358    0.01877626642906      H
    4.27571474378505    -1.92854948200207    9.94745802440185      N
    4.85863257632589    -1.86976812841619   11.77386435287947      H
    2.41997661925239    -2.42173187608252    9.97254129755107      H
    4.53188129867197     0.54201882289930    8.80305477310553      C
    3.10180400437508     2.58147803262171   10.25033240656862      C
    1.70252284002797     2.17538275447565   11.99395863899712      O
    3.59502480456652     4.91081582322646    9.40273172353399      O
    2.64101197107364     6.15144169604561   10.36051515045620      H
    6.53940694073007     1.05972961089276    8.80707208579245      H
    3.60684313919014     0.48755395354171    6.03553367623200      C
    0.79623558975634     0.11581314423023    5.88366583446487      C
    -0.24093223813749   -2.29403771457139    5.84928985318257      C
    -2.83094211079699   -2.64168158463332    5.81583719831421      C
    -4.43914545143533   -0.56757465165303    5.80885193908835      C
    -3.41896413800189    1.85508153404960    5.82002566936256      C
    -0.83164012890154    2.17804731008809    5.85479160455166      C
    -0.06058114066044    4.06926172450655    5.83858398852997      H
    -4.68432097650001    3.45280350209968    5.79576231758199      H
    -6.99839493428426   -0.81481618645066    5.77227418763592      O
    -7.44727356719986   -2.58190479542918    5.74085372355529      H
    -3.61086295708159   -4.53297500622820    5.78522163995966      H
    0.99207739459520    -3.92144387056497    5.83721740609899      H
    4.58691246909114    -1.06321033030212    5.09739729211277      H
    4.13984012793008     2.26724282543661    5.14389351386854      H
    $end

crest coord -v3 -T 40 -subrmsd -nozs -shake 0 -tstep 1 > crest.out

# for convergence reasons the md settings were adjusted.
# the file .constrains is found automatically