crest - Man Page

Conformer-Rotamer Ensemble Sampling Tool based on the GFN methods

Synopsis

crest [INPUT] [OPTION]...

Description

Conformer-Rotamer Ensemble Sampling Tool based on the GFN methods.

Using the xTB program. Compatible with xTB version 6.4.0.

Cite work conducted with this code as

 P. Pracht, F. Bohle, S. Grimme, PCCP, 2020, 22, 7169-7192.

 and  S. Grimme, JCTC, 2019, 15, 2847-2862.

 with help from:
 F.Bohle, S.Ehlert, S.Grimme, P.Pracht

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Options

The FIRST argument CAN be a coordinate file in the TM (coord, Bohr) or Xmol (*.xyz, Ang.) format. If no such file is present as the first argument crest will automatically search for a file called “coord” in the TM format.

General and technical options

-v1

Use the MF-MD-GC workflow. (OUTDATED)

-v2

Use the MTD-GC workflow. (OUTDATED)

-v3 (or -v2i)

Use the iMTD-GC workflow. [default]

-v4

Use the iMTD-sMTD workflow.

-entropy

The same workflow as with “-v4”, specialized for the calculation of conformational entropy.

-xnam bin

Specify name of the xtb(1) binary that should be used.

-niceprint

Progress bar printout for optimizations.

-dry

Perform a “dry run”. Only prints the settings that would be applied with the CMD input and stops the run before any calculations

-T int

Set total number of CPUs (threads) to be used. Parallel settings are then determined automatically for each step. If not set by “-T”, this number is read from the OMP_NUM_THREADS global variable.

Calculation options

-g string

Use GBSA implicit solvent for solvent string.

-alpb string

Use ALPB implicit solvent for solvent string.

-chrg int

Set the molecules’ charge.

-uhf int

Set int=N alpha - N beta electrons

-nozs

Do not perform z-mat sorting. [default]

-opt lev

Set optimization level for ALL GFN-xTB optimizations. [default: vtight]

  • lev = vloose, loose, normal, tight, vtight
-gfn1

Use GFN1-xTB.

-gfn2

Use GFN2-xTB. [default]

-gff,  -gfnff

Use GFN-FF (requires xtb(1) 6.3 or newer). (For GFN-FF searches bond constraints are applied automatically.)

-gfn2//gfnff

GFN2-xTB//GFN-FF composite mode.

Adding additional constraints to the calculations:

The user is able to include additional constraints to ALL xtb(1) calculations that are conducted by CREST.

-cinp file

Read in a file containing the constraints. Constraints have to be in the same format as in xtb(1). (This was done previously via the “.constrains” file.)

-cbonds

Define automatic bond constraints (set up from topology).

-nocbonds

Turn off -cbonds. (For GFN-FF, mainly. See above.)

-fc float

Define force constant for defined constraints (-cbonds).

Options for ensemble comparisons

-cregen file

Use ONLY the CREGEN subroutine to sort a given ensemble file.

-ewin real

Set energy window in kcal/mol. [default: 6.0 kcal/mol]

-rthr real

Set RMSD threshold in Ang. [default: 0.125 Ang]

-ethr real

Set E threshold in kcal/mol. [default: 0.05 kcal/mol]

-bthr real

Set Rot. const. threshold. [default: 0.01 (= 1%)]

-pthr real

Boltzmann population threshold. [default: 0.05 (= 5%)]

-temp real

Set temperature in CREGEN. [default: 298.15 K]

-prsc

Create a scoord.* file for each conformer.

-nowr

Don’t write new ensemble files.

-eqv,-nmr,-entropy

Compare nuclear equivalences (requires rotamers).

-cluster int

PCA and k-Means clustering of sorted ensemble. Works as extenstion to the CREGEN sorting. int is the number of clusters to be formed.

-notopo

Turn off any topology checks in CREGEN.

Options for the iMTD-GC workflows

-cross

Do the GC part. [default]

-nocross

Don’t do the GC part.

-shake int

Set SHAKE mode for MD. (0=off, 1=H-only, 2=all bonds) [default: 2]

-tstep int

Set MD time step in fs. [default: 5 fs]

-mdlen/-len real

Set MD length (all MTDs) in ps. Also possible are multiplicative factors for the default MD length with “xreal”.

-mddump int

xyz dumpstep to Trajectory in fs. [default: 100 fs]

-vbdump real

Set Vbias dump frequency in ps. [default: 1.0 ps]

-tnmd real

Set temperature for additional normal MDs. [default: 400 K]

-norotmd

Don’t do the regular MDs after the second multilevel optimization step.

-quick

Perform a search with reduced settings for a crude ensemble.

-squick

Perform a even further reduced search.

-mquick

Perform a search with maximum reduced settings. (Do not reduce the settings more than that.)

-origin

Track the step of generation for each conformer/rotamer. [default]

-keepdir

Keep sub-directories of the conformer generation step.

-nci

Generate an ellipsoide potential around the input structure and add it to the MTD simulation. This can be used to find aggregates of NCI complexes.

-wscal real

Scale the ellipsoide potential axes by factor real.

Thermostatistical options (used in entropy mode)

-trange lower upper step

Entropies are calculated for different temperatures. These are calculated in a temperature range from lower to upper with step in between. [default: 280K-380K in 10K steps]

-fscal float

Frequency scaling factor. [default: 1.0]

-sthr float

Vibrational/rotational entropy interpolation threshold (tau). [default: 25.0 cm^-1]

-ithr float

Imaginary mode inversion cutoff. [default: -50.0 cm^-1]

-ptot float

Sum of population for structures considered in msRRHO average. [default: 0.9 (= 90%)]

Other tools for standalone use

-zsort

Use only the zsort subroutine to sort the z-matrix of the input coordinate file.

-mdopt file

Optimize along trajectory or ensemble file in the XYZ format. Each point on the file is optimized.

-screen file

Optimize along ensemble file in the XYZ format. A multilevel optimization is performed with continiously increasing thresholds. After each step the ensemble file is sorted.

-protonate

Find a molecule’s protomes by using a LMO pi- or LP-center approach.

-deprotonate

Find a molecule’s deprotomers.

-tautomerize

Combine the protonation and deprotonation to find prototropic tautomers.

-trev

Do first the deprotonation and then the protonation in the -tautomerize mode, i.e., reverse of the default procedure.

-iter int

Set number of protonation/deprotonation cycles in the tautomerization script. [default: 2]

-compare f1 f2

Compare two ensembles f1 and f2. Both ensembles must have the same order of atoms of the molecule and should contain rotamers.

-maxcomp int

Select the lowest int conformers out of each ensemble to be compared with “-compare”. [default: 10]

-testtopo file

Analyze some stuctural info (topology) for a given file.

-constrain atoms

Write example file “.xcontrol.sample” for constraints in crest. (See -cinp option above.)

-thermo file

Calculate thermo data for given structure. Also requires vibrational frequencies in the TM format, saved as file called “vibspectrum”.

-rmsd,-rmsdheavy file1 file2

Calculate RMSD or heavy atom RMSD between two structures. Input coords are automatically transformed to Angstroem.

-splitfile file [from] [to]

Split an ensemble from file into seperate directories for each structure. from and to can be used to select specific structures from the file. The new directories are collected in the SPLIT directory.

Notes

View literature references with --cite.

Authors

P.Pracht

S.Grimme

Universitaet Bonn, MCTC

Info

2022-07-20 Crest 2.11.0