1CREST(1) User Commands CREST(1)
2
6 crest - Conformer-Rotamer Ensemble Sampling Tool based on the GFN
7 methods
8
10 crest [INPUT] [OPTION]...
11
13 Conformer-Rotamer Ensemble Sampling Tool based on the GFN methods.
14 Using the xTB program. Compatible with xTB version 6.4.0.
16 Cite work conducted with this code as
18 P. Pracht, F. Bohle, S. Grimme, PCCP, 2020, 22, 7169-7192.
20 and S. Grimme, JCTC, 2019, 15, 2847-2862.
22 with help from:
24 F.Bohle, S.Ehlert, S.Grimme, P.Pracht
25 This program is distributed in the hope that it will be useful, but
27 WITHOUT ANY WARRANTY; without even the implied warranty of
28 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
29
31 The FIRST argument CAN be a coordinate file in the TM (coord, Bohr) or
32 Xmol (*.xyz, Ang.) format. If no such file is present as the first
33 argument crest will automatically search for a file called “coord” in
34 the TM format.
35 General and technical options
37 -v1
38 Use the MF-MD-GC workflow. (OUTDATED)
39 -v2
41 Use the MTD-GC workflow. (OUTDATED)
42 -v3 (or -v2i)
44 Use the iMTD-GC workflow. [default]
45 -v4
47 Use the iMTD-sMTD workflow.
48 -entropy
50 The same workflow as with “-v4”, specialized for the calculation of
51 conformational entropy.
52 -xnam bin
54 Specify name of the xtb(1) binary that should be used.
55 -niceprint
57 Progress bar printout for optimizations.
58 -dry
60 Perform a “dry run”. Only prints the settings that would be applied
61 with the CMD input and stops the run before any calculations
62 -T int
64 Set total number of CPUs (threads) to be used. Parallel settings
65 are then determined automatically for each step. If not set by
66 “-T”, this number is read from the OMP_NUM_THREADS global variable.
67 Calculation options
69 -g string
70 Use GBSA implicit solvent for solvent string.
71 -alpb string
73 Use ALPB implicit solvent for solvent string.
74 -chrg int
76 Set the molecules’ charge.
77 -uhf int
79 Set int=N alpha - N beta electrons
80 -nozs
82 Do not perform z-mat sorting. [default]
83 -opt lev
85 Set optimization level for ALL GFN-xTB optimizations. [default:
86 vtight]
87 • lev = vloose, loose, normal, tight, vtight
89 -gfn1
91 Use GFN1-xTB.
92 -gfn2
94 Use GFN2-xTB. [default]
95 -gff, -gfnff
97 Use GFN-FF (requires xtb(1) 6.3 or newer). (For GFN-FF searches
98 bond constraints are applied automatically.)
99 -gfn2//gfnff
101 GFN2-xTB//GFN-FF composite mode.
102 Adding additional constraints to the calculations:
104 The user is able to include additional constraints to ALL xtb[1m(1)
106 calculations that are conducted by CREST.
107 -cinp file
109 Read in a file containing the constraints. Constraints have to be
110 in the same format as in xtb[1m(1). (This was done previously via the
111 “.constrains” file.)
112 -cbonds
114 Define automatic bond constraints (set up from topology).
115 -nocbonds
117 Turn off -cbonds. (For GFN-FF, mainly. See above.)
118 -fc float
120 Define force constant for defined constraints (-cbonds).
121 Options for ensemble comparisons
123 -cregen file
124 Use ONLY the CREGEN subroutine to sort a given ensemble file.
125 -ewin real
127 Set energy window in kcal/mol. [default: 6.0 kcal/mol]
128 -rthr real
130 Set RMSD threshold in Ang. [default: 0.125 Ang]
131 -ethr real
133 Set E threshold in kcal/mol. [default: 0.05 kcal/mol]
134 -bthr real
136 Set Rot. const. threshold. [default: 0.01 (= 1%)]
137 -pthr real
139 Boltzmann population threshold. [default: 0.05 (= 5%)]
140 -temp real
142 Set temperature in CREGEN. [default: 298.15 K]
143 -prsc
145 Create a scoord.* file for each conformer.
146 -nowr
148 Don’t write new ensemble files.
149 -eqv,-nmr,-entropy
151 Compare nuclear equivalences (requires rotamers).
152 -cluster int
154 PCA and k-Means clustering of sorted ensemble. Works as extenstion
155 to the CREGEN sorting. int is the number of clusters to be formed.
156 -notopo
158 Turn off any topology checks in CREGEN.
159 Options for the iMTD-GC workflows
161 -cross
162 Do the GC part. [default]
163 -nocross
165 Don’t do the GC part.
166 -shake int
168 Set SHAKE mode for MD. (0=off, 1=H-only, 2=all bonds) [default: 2]
169 -tstep int
171 Set MD time step in fs. [default: 5 fs]
172 -mdlen/-len real
174 Set MD length (all MTDs) in ps. Also possible are multiplicative
175 factors for the default MD length with “xreal”.
176 -mddump int
178 xyz dumpstep to Trajectory in fs. [default: 100 fs]
179 -vbdump real
181 Set Vbias dump frequency in ps. [default: 1.0 ps]
182 -tnmd real
184 Set temperature for additional normal MDs. [default: 400 K]
185 -norotmd
187 Don’t do the regular MDs after the second multilevel optimization
188 step.
189 -quick
191 Perform a search with reduced settings for a crude ensemble.
192 -squick
194 Perform a even further reduced search.
195 -mquick
197 Perform a search with maximum reduced settings. (Do not reduce the
198 settings more than that.)
199 -origin
201 Track the step of generation for each conformer/rotamer. [default]
202 -keepdir
204 Keep sub-directories of the conformer generation step.
205 -nci
207 Generate an ellipsoide potential around the input structure and add
208 it to the MTD simulation. This can be used to find aggregates of
209 NCI complexes.
210 -wscal real
212 Scale the ellipsoide potential axes by factor real.
213 Thermostatistical options (used in entropy mode)
215 -trange lower upper step
216 Entropies are calculated for different temperatures. These are
217 calculated in a temperature range from lower to upper with step in
218 between. [default: 280K-380K in 10K steps]
219 -fscal float
221 Frequency scaling factor. [default: 1.0]
222 -sthr float
224 Vibrational/rotational entropy interpolation threshold (tau).
225 [default: 25.0 cm^-1]
226 -ithr float
228 Imaginary mode inversion cutoff. [default: -50.0 cm^-1]
229 -ptot float
231 Sum of population for structures considered in msRRHO average.
232 [default: 0.9 (= 90%)]
233 Other tools for standalone use
235 -zsort
236 Use only the zsort subroutine to sort the z-matrix of the input
237 coordinate file.
238 -mdopt file
240 Optimize along trajectory or ensemble file in the XYZ format. Each
241 point on the file is optimized.
242 -screen file
244 Optimize along ensemble file in the XYZ format. A multilevel
245 optimization is performed with continiously increasing thresholds.
246 After each step the ensemble file is sorted.
247 -protonate
249 Find a molecule’s protomes by using a LMO pi- or LP-center
250 approach.
251 -deprotonate
253 Find a molecule’s deprotomers.
254 -tautomerize
256 Combine the protonation and deprotonation to find prototropic
257 tautomers.
258 -trev
260 Do first the deprotonation and then the protonation in the
261 -tautomerize mode, i.e., reverse of the default procedure.
262 -iter int
264 Set number of protonation/deprotonation cycles in the
265 tautomerization script. [default: 2]
266 -compare f1 f2
268 Compare two ensembles f1 and f2. Both ensembles must have the same
269 order of atoms of the molecule and should contain rotamers.
270 -maxcomp int
272 Select the lowest int conformers out of each ensemble to be
273 compared with “-compare”. [default: 10]
274 -testtopo file
276 Analyze some stuctural info (topology) for a given file.
277 -constrain atoms
279 Write example file “.xcontrol.sample” for constraints in crest.
280 (See -cinp option above.)
281 -thermo file
283 Calculate thermo data for given structure. Also requires
284 vibrational frequencies in the TM format, saved as file called
285 “vibspectrum”.
286 -rmsd,-rmsdheavy file1 file2
288 Calculate RMSD or heavy atom RMSD between two structures. Input
289 coords are automatically transformed to Angstroem.
290 -splitfile file [from] [to]
292 Split an ensemble from file into seperate directories for each
293 structure. from and to can be used to select specific structures
294 from the file. The new directories are collected in the SPLIT
295 directory.
296
298 View literature references with --cite.
299
301 P.Pracht
302 S.Grimme
304 Universitaet Bonn, MCTC
306Crest 2.11.0 2022-07-20 CREST(1)