[gmx-users] topolbuild ( Failing to read oxygen in H2O )
David van der Spoel
spoel at xray.bmc.uu.se
Sat Nov 26 10:26:57 CET 2016
On 26/11/16 09:24, 大木啓輔 wrote:
> Dear gromacs users
>
> I have a question why topolbuild fails to read oxygen in H2O.
>
> I want to make a topology file of methane hydrate structure with topolbuild and run simulation in gromacs.
>
For these simple molecules you want hand-tuned force fields not
automatically generated stuff. That mean writing the topologies your
self, and choosing a standard water model, e.g. TIP4P or TIP4P/Ice for
your application.
> I used following command line:
>
> ./topolbuild -n ../HYDRATE_A -dir ../dat/gromacs -ff oplsaa -purge 0
>
> .mol2 file that I used then {
>
> @<TRIPOS>MOLECULE
> ch4h2o_4.pdb
> 46 36 10 0 0
> SMALL
> USER_CHARGES
>
>
> @<TRIPOS>ATOM
> 1 C 5.6060 1.6670 5.1720 C.3 1 LIG1 -0.4588
> 2 H 6.2390 2.2990 5.8040 H 1 LIG1 0.1147
> 3 H 4.9740 1.0350 5.8040 H 1 LIG1 0.1147
> 4 H 4.9740 2.2990 4.5400 H 1 LIG1 0.1147
> 5 H 6.2390 1.0350 4.5400 H 1 LIG1 0.1147
> :
> 41 O 7.0060 1.7150 8.9340 O.3 9 H2O -1.1794
> 42 H 6.0130 1.7150 9.0510 H 9 H2O 0.5897
> 43 H 7.4440 1.7150 9.8330 H 9 H2O 0.5897
> 44 O 6.9570 1.7200 1.4090 O.3 10 H2O -1.1794
> 45 H 7.2050 0.8780 1.8880 H 10 H2O 0.5897
> 46 H 7.2400 2.5080 1.9570 H 10 H2O 0.5897
> @<TRIPOS>BOND
> 1 1 2 1
> 2 1 3 1
> 3 1 4 1
> 4 1 5 1
> :
> 33 41 42 1
> 34 41 43 1
> 35 44 45 1
> 36 44 46 1
> @<TRIPOS>SUBSTRUCTURE
> 1 LIG1 1 RESIDUE 4 A LIG1 0 ROOT
> 2 LIG1 6 RESIDUE 4 A LIG1 0 ROOT
> 3 LIG1 11 RESIDUE 4 A LIG1 0 ROOT
> 4 LIG1 16 RESIDUE 4 A LIG1 0 ROOT
> 5 LIG1 21 RESIDUE 4 A LIG1 0 ROOT
> 6 LIG1 26 RESIDUE 4 A LIG1 0 ROOT
> 7 LIG1 31 RESIDUE 4 A LIG1 0 ROOT
> 8 LIG1 36 RESIDUE 4 A LIG1 0 ROOT
> 9 H2O 41 RESIDUE 4 A H2O 0 ROOT
> 10 H2O 44 RESIDUE 4 A H2O 0 ROOT
>
> }
>
> ( this file was used for trial, so this is not hydrate structure )
>
> Then, I got this topology file {
>
> ; The force field files to be included
> #include "ffHYDRATE_A.itp"
>
> [ moleculetype ]
> ; name nrexcl
> ch4h2o_4.pdb 3
>
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass
> 1 opls_138 1 LIG C 1 -0.45880 12.01100 ; -0.4588000
> 2 opls_140 1 LIG H 1 0.11470 1.00800 ; -0.3441000
> 3 opls_140 1 LIG H 1 0.11470 1.00800 ; -0.2294000
> 4 opls_140 1 LIG H 1 0.11470 1.00800 ; -0.1147000
> 5 opls_140 1 LIG H 1 0.11470 1.00800 ; 0.0000000
> :
> 41 O?? 9 H2O O 9 -1.17940 15.99940 ; -1.1794000
> 42 opls_435 9 H2O H 10 0.58970 1.00800 ; -0.5897000
> 43 opls_435 9 H2O H 11 0.58970 1.00800 ; 0.0000000
> 44 O?? 10 H2O O 12 -1.17940 15.99940 ; -1.1794000
> 45 opls_435 10 H2O H 13 0.58970 1.00800 ; -0.5897000
> 46 opls_435 10 H2O H 14 0.58970 1.00800 ; 0.0000000
> ; total molecule charge = 0.0000000
>
> [ bonds ]
> ; ai aj funct b0 kb
> 1 2 1 0.10900 284512. ; C- H
> 1 3 1 0.10900 284512. ; C- H
> 1 4 1 0.10900 284512. ; C- H
> 1 5 1 0.10900 284512. ; C- H
> :
> 41 42 ; O- H
> 41 43 ; O- H
> 44 45 ; O- H
> 44 46 ; O- H
>
> [ pairs ]
>
> [ angles ]
> ; ai aj ak funct th0 cth
> 3 1 2 1 107.800 276.1440 ; H- C- H
> 4 1 2 1 107.800 276.1440 ; H- C- H
> 5 1 2 1 107.800 276.1440 ; H- C- H
> :
> 43 41 42 ; H- O- H
> 46 44 45 ; H- O- H
>
> }
>
> I tried other input files with changing O.3 to (O.spc and H.spc) and (O.t3p and H.t3p) ,
> but force field types of oxygen in H2O were not read.
>
> Why this problem was occurred?
> Should I fix this topology file?
>
> Could you tell me this problem solution, please?
>
>
>
>
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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