pprcht
commented
4 years ago We are not planning to release to full update yet, but a development version of crest is available here, in which --alpb <solvent> can be used.
Closed lizhiq16 closed 2 years ago
pprcht
commented
4 years ago We are not planning to release to full update yet, but a development version of crest is available here, in which --alpb <solvent> can be used.
xiki-tempula
commented
3 years ago I have tried to use this crest to deprotonated the tert-butyl alcohol (m_01.sdf)
6386
-OEChem-12292005403D
15 14 0 0 0 0 0 0 0999 V2000
0.0001 0.0886 1.4263 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.0001 -0.0042 0.0012 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2740 -0.7243 -0.4388 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0316 1.4186 -0.5526 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2423 -0.7788 -0.4361 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1666 -0.1866 -0.0991 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3246 -0.8252 -1.5278 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3276 -1.7245 0.0059 H 0 0 0 0 0 0 0 0 0 0 0 0
0.9155 1.9576 -0.1927 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.8390 1.9921 -0.2141 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0439 1.4248 -1.6474 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2468 -1.7838 0.0007 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2975 -0.8731 -1.5255 H 0 0 0 0 0 0 0 0 0 0 0 0
2.1543 -0.2842 -0.0826 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7978 0.5741 1.6975 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 15 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
2 5 1 0 0 0 0
3 6 1 0 0 0 0
3 7 1 0 0 0 0
3 8 1 0 0 0 0
4 9 1 0 0 0 0
4 10 1 0 0 0 0
4 11 1 0 0 0 0
5 12 1 0 0 0 0
5 13 1 0 0 0 0
5 14 1 0 0 0 0
M END
> <PUBCHEM_COMPOUND_CID>
6386
> <PUBCHEM_CONFORMER_RMSD>
0.4
> <PUBCHEM_CONFORMER_DIVERSEORDER>
1
> <PUBCHEM_MMFF94_PARTIAL_CHARGES>
3
1 -0.68
15 0.4
2 0.28
> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>
0
> <PUBCHEM_PHARMACOPHORE_FEATURES>
3
1 1 acceptor
1 1 donor
4 2 3 4 5 hydrophobe
> <PUBCHEM_HEAVY_ATOM_COUNT>
5
> <PUBCHEM_ATOM_DEF_STEREO_COUNT>
0
> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
0
> <PUBCHEM_BOND_DEF_STEREO_COUNT>
0
> <PUBCHEM_BOND_UDEF_STEREO_COUNT>
0
> <PUBCHEM_ISOTOPIC_ATOM_COUNT>
0
> <PUBCHEM_COMPONENT_COUNT>
1
> <PUBCHEM_CACTVS_TAUTO_COUNT>
1
> <PUBCHEM_CONFORMER_ID>
000018F200000001
> <PUBCHEM_MMFF94_ENERGY>
8.0669
> <PUBCHEM_FEATURE_SELFOVERLAP>
15.223
> <PUBCHEM_SHAPE_FINGERPRINT>
20096714 4 9405031127561521575
21015797 1 16608521968230149127
5943 1 11462338020108140573
> <PUBCHEM_SHAPE_MULTIPOLES>
97.03
1.27
1.27
1.04
0.04
0.46
-0.4
-0.49
0.28
-0.04
0.3
0
0.02
0
> <PUBCHEM_SHAPE_SELFOVERLAP>
167.995
> <PUBCHEM_SHAPE_VOLUME>
66.7
> <PUBCHEM_COORDINATE_TYPE>
2
5
10
$$$$By using the cmd
xtb-6.3.3/bin/crest m_01.sdf -deprotonate --alpb h2o
However, I got
==============================================
| |
| C R E S T |
| |
| Conformer-Rotamer Ensemble Sampling Tool |
| based on the GFN methods |
| P.Pracht, S.Grimme |
| Universitaet Bonn, MCTC |
==============================================
Version 2.11dev, Tue 13. Oct 10:57:46 CEST 2020
Using the xTB program. Compatible with xTB version 6.3.3
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.
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.
Command line input:
> /biggin/b120/grte2001/src/xtb-6.3.3/bin/crest m_01.sdf -deprotonate --alpb h2o
molecular charge read from .CHRG: -3
-deprotonate : automated deprotonation script
--alpb h2o : implicit solvation
=============================
# threads = 1
=============================
__________________________________________
| |
| automated deprotonation script |
|__________________________________________|
Universitaet Bonn, MCTC
P.Pracht, Wed 28. Nov 13:11:52 CEST 2018
-----------------------
Multilevel Optimization
-----------------------
-------------------------
1. crude pre-optimization
-------------------------
Optimizing all 10 structures from file "deprotonate_0.xyz" ...
forrtl: severe (124): Invalid command supplied to EXECUTE_COMMAND_LINE
Image PC Routine Line Source
crest 00000000027577CD Unknown Unknown Unknown
crest 0000000000525DD3 Unknown Unknown Unknown
crest 0000000002894E1F Unknown Unknown Unknown
crest 0000000002895739 Unknown Unknown Unknown
crest 000000000288F4DF Unknown Unknown Unknown
crest 0000000000526D9B Unknown Unknown Unknown
crest 00000000028A4863 Unknown Unknown Unknown
crest 0000000002866115 Unknown Unknown Unknown
crest 0000000002830025 Unknown Unknown Unknown
crest 0000000000524645 Unknown Unknown Unknown
crest 00000000005CCC06 Unknown Unknown Unknown
crest 00000000004C3C09 Unknown Unknown Unknown
crest 00000000005DB915 Unknown Unknown Unknown
crest 00000000004047D2 Unknown Unknown Unknown
crest 00000000029583B0 Unknown Unknown Unknown
crest 00000000004046B7 Unknown Unknown Unknown
The analytical linearized Poisson-Boltzmann (ALPB) model is the default solvation model for xtb-6.3.3. I wonder how can I use ALPB in crest? if not, I guess some change may be needed in crest's code. thanks.