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 (OUTDATED)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 (OUTDATED)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