[gmx-users] topolbuild ( Failing to read oxygen in H2O )
大木啓輔
keisuke.ohki at keio.jp
Tue Nov 29 03:26:20 CET 2016
Dear Bruce D. Ray
Thank you for replying to my question.
I understood that I should not include water molecules in submit file to topolbuild
because water topology is given by spce.itp.
Then, should I give coordinates of water to *.gro file and delete parameters of water in topology file
when hydrate structure is the object of my study?
Sincerely.
Keisuke Ohki
> 2016/11/29 3:45、Ray, Bruce D <bray at iupui.edu>のメール:
>
> 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
>
>
> --
> Gromacs Users mailing list
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