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Comments (2)

pprcht avatar pprcht commented on May 29, 2024

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.

from crest.

xiki-tempula avatar xiki-tempula commented on May 29, 2024

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

from crest.

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