[gmx-users] topolbuild ( Failing to read oxygen in H2O )
Ray, Bruce D
bray at iupui.edu
Tue Nov 29 15:09:55 CET 2016
On Nov 28, 2016, at 9:26 PM, ???? <keisuke.ohki at keio.jp> wrote:
> Date: Tue, 29 Nov 2016 11:26:08 +0900
> From: ???? <keisuke.ohki at keio.jp>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] topolbuild ( Failing to read oxygen in H2O )
> Message-ID: <C1B704EF-958E-491A-A0A2-834994C1B150 at keio.jp>
> Content-Type: text/plain; charset=utf-8
>
> 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>????:
>>
>> 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.
If you do not have any waters in the *.mol2 file of the molecule for which a topology
is to be built that you give to topolbuild, then there will not be any water parameters
in the output from topolbuild and deletions in the topology file will not be needed.
Building the final *.gro file may require use of a text editor followed by the gromacs
utilities for configuration editing, solvating the box, adding ions, and so forth.
Building the topology of the final system may require use of a text editor before
submitting the topology to appropriate gromacs utilities along with the *.gro file.
Those are issues outside of the scope of topolbuild
--
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN 46202
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