[gmx-users] topolbuild ( Failing to read oxygen in H2O )
Ray, Bruce D
bray at iupui.edu
Mon Nov 28 19:46:01 CET 2016
On Nov 26, 2016, at 4:19 AM, ???? <keisuke.ohki at keio.jp> wrote:
> Date: Sat, 26 Nov 2016 17:24:56 +0900
> From: ???? <keisuke.ohki at keio.jp>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] topolbuild ( Failing to read oxygen in H2O )
> Message-ID: <07C401C0-1755-433C-9E89-C7A9E8A87F0E at keio.jp>
> Content-Type: text/plain; charset=us-ascii
>
> 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.
>
> 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?
Edit your input so that you only give the molecule of interest without the waters.
Your starting file has two waters and a ligand in it. topolbuild is designed to
generate a topology from a file that contains one molecule. Water topologies are
already provided for each force field and do not need to be generated with topolbuild
Thus, you should never include waters in the file submitted to topolbuild
For this same reason, the special oxygen and hydrogen types used for water topologies
are not included in the topolbuild files. Thus, for OPLSAA, where spc.itp specifies
opls_111 for water oxygen, and opls_112 for water hydrogen, neither is provided in
topolbuild.
--
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN 46202
More information about the gromacs.org_gmx-users
mailing list