[gmx-users] Multiple chains, cofactors and ligands--ffgmx unreliable?
Yang Ye
leafyoung81-group at yahoo.com
Fri Feb 3 19:32:59 CET 2006
opls-aa
YOLANDA SMALL wrote:
> Thanks to Daniela, Yang and Tsjerk for a reply...your advice was helpful.
>
> Tsjerk, you were exactly correct, I did have multiple listings of the directive
> in my ligand and ions .itp files. But now you raise a point that concerns
> me....why is ffgmx not reliable?
>
> I always check the energies and structures for unusual behavior throughout the
> simulations. How does this unreliability manifest itself? Which is the most
> highly recommended forcefield option in the gmx package?
>
> Many thanks,
> YAS
>
> On Fri, 03 Feb 2006 09:37:27 +0100, Tsjerk Wassenaar wrote:
>
>
>> Hi Yolanda,
>>
>> And then for the solution to your problem... The error in grompp indicates
>> that you call the force field defaults directive (ffgmx.itp) several times.
>> Probably, the prodrg server has added a statement similar to #include "
>> ffgmx.itp" to the itp files for the ligand and the cofactor. You should
>> delete those statements, which will probably solve the error.
>>
>> By the way, the ffgmx force field isn't particularly reliable.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On 2/3/06, Yang Ye <leafyoung81-group at yahoo.com> wrote:
>>
>>> Run GMXRC.xxx according to the shell you are using before running gromacs
>>> programs.
>>>
>>> Yang Ye
>>>
>>> -----Original Message-----
>>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
>>> On Behalf Of YOLANDA SMALL
>>> Sent: Friday, February 03, 2006 1:12 AM
>>> To: Discussion list for GROMACS users
>>> Subject: [gmx-users] Multiple chains, cofactors and ligands
>>>
>>> Dear users,
>>>
>>> I am having a problem with grompp which gives me the following message:
>>> Fatal error: Invalid order for directive defaults, file
>>> ""/gromacs-3.2.1/share/top/ffgmx.itp"", line 4
>>>
>>> My simulation details:
>>> An enzyme with 2 chains, 2 cofactors and 2 ligands in a 115 Angstrom box
>>> of
>>> SPC
>>> waters. The total system size is 150872 atoms. Each chain has a separate
>>> .itp
>>> file created with pdb2gmx. Each cofactor and ligand has an .itp file
>>> created
>>> with PRODRG. The files are joined in the following topology file:
>>>
>>> ; Include forcefield parameters
>>> #include "ffgmx.itp"
>>>
>>> ; Include chain topologies
>>> #include "chain_A.itp"
>>> #include "chain_B.itp"
>>> #include "cofactor_A.itp"
>>> #include "cofactor_B.itp"
>>> #include "ligand_A.itp"
>>> #include "ligand_B.itp"
>>> #include "Na.itp"
>>>
>>> ; Include water topology
>>> #include "spc.itp"
>>>
>>> ; Include generic topology for ions
>>> #include "ions.itp"
>>>
>>> [ system ]
>>> ; Name
>>> 2 COMPLEXED WITH (Ligand)
>>>
>>> [ molecules ]
>>> ; Compound #mols
>>> Protein_A 1
>>> Protein_B 1
>>> SOL 346
>>> COF_A 1
>>> COF_B 1
>>> LIG_A 1
>>> LIG_B 1
>>> NA 1
>>> SOL 47872
>>>
>>> The problem:
>>> I only get this message when the topology of the cofactor and ligand are
>>> included. When I run the simulation on the protein chains only without
>>> the
>>> ligand and cofactor, it runs just fine. I double-checked the topology of
>>> the
>>> ligand and cofactor and I don't see any errors. Do I need to change the
>>> defaults in the following ffgmx.itp file to get this to work???? (The
>>> error
>>> message points to line 4 of this file) If so, what should I change the
>>> defaults to?
>>>
>>> #define _FF_GROMACS
>>> #define _FF_GROMACS1
>>>
>>> [ defaults ]
>>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>>> 1 1 no 1.0 1.0
>>>
>>> #include "ffgmxnb.itp"
>>> #include "ffgmxbon.itp"
>>>
>>> Thanks in advance for your help,
>>> YAS
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
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>>>
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>>> gmx-users mailing list gmx-users at gromacs.org
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>>>
>>
>> --
>>
>> Tsjerk A. Wassenaar, M.Sc.
>> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
>> Dept. of Biophysical Chemistry
>> University of Groningen
>> Nijenborgh 4
>> 9747AG Groningen, The Netherlands
>> +31 50 363 4336
>> Hi Yolanda,
>>
>> And then for the solution to your problem... The error in grompp
>> indicates that you call the force field defaults directive (ffgmx.itp)
>> several times. Probably, the prodrg server has added a statement
>> similar to #include "ffgmx.itp" to the itp files for the ligand and the
>> cofactor. You should delete those statements, which will probably solve
>> the error.
>>
>> By the way, the ffgmx force field isn't particularly reliable.
>>
>> Cheers,
>>
>> TsjerkOn 2/3/06, Yang Ye <leafyoung81-group at yahoo.com> wrote:
>> Run GMXRC.xxx according to the shell you are using before running
>>
> gromacsprograms.Yang Ye-----Original Message-----From:
> gmx-users-bounces at gromacs.org
>
>> [mailto:gmx-users-bounces at gromacs.org]On Behalf Of YOLANDA SMALLSent: Friday,
>>
> February 03, 2006 1:12 AMTo: Discussion list for GROMACS usersSubject:
> [gmx-users] Multiple chains, cofactors and ligands
>
>> Dear users,I am having a problem with grompp which gives me the following
>>
> message:Fatal error: Invalid order for directive defaults,
> file""/gromacs-3.2.1/share/top/ffgmx.itp"", line 4
>
>> My simulation details:An enzyme with 2 chains, 2 cofactors and 2 ligands in a
>>
> 115 Angstrom box ofSPCwaters. The total system size is 150872 atoms. Each
> chain has a separate.itpfile created with pdb2gmx. Each cofactor and ligand has
> an .itp file created
>
>> with PRODRG. The files are joined in the following topology file:; Include
>>
> forcefield parameters#include "ffgmx.itp"; Include chain topologies#include
> "chain_A.itp"#include "chain_B.itp"
>
>> #include "cofactor_A.itp"#include "cofactor_B.itp"#include
>>
> "ligand_A.itp"#include "ligand_B.itp"#include "Na.itp"; Include water
> topology#include "
>
>> spc.itp"; Include generic topology for ions#include "ions.itp"[ system ];
>>
> Name2 COMPLEXED WITH (Ligand)[ molecules ]; Compound #molsProtein_A
> 1
>
>> Protein_B 1SOL 346COF_A 1COF_B
>>
> 1LIG_A 1LIG_B 1NA 1SOL
> 47872The problem:I only get this message when the topology of the cofactor
> and ligand are
>
>> included. When I run the simulation on the protein chains only without
>>
> theligand and cofactor, it runs just fine. I double-checked the topology
> oftheligand and cofactor and I don't see any errors. Do I need to change the
>
>> defaults in the following ffgmx.itp file to get this to work???? (The
>>
> errormessage points to line 4 of this file) If so, what should I change
> thedefaults to?#define _FF_GROMACS#define _FF_GROMACS1
>
>> [ defaults ];
>> nbfunc comb-rule
>> gen-pairs fudgeLJ fudgeQQ 1
>> 1
>> no 1.0
>> 1.0#include "ffgmxnb.itp"#include "ffgmxbon.itp"Thanks in advance for your
>>
> help,YAS_______________________________________________gmx-users mailing list
>
>
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>>
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> send it to gmx-users-request at gromacs.org.Can't post? Read
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>> http://www.gromacs.org/mailing_lists/users.php-- Tsjerk A. Wassenaar,
>>
> M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of
> Biophysical Chemistry
>
>> University of GroningenNijenborgh 49747AG Groningen, The Netherlands+31 50 363
>>
> 4336
>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>>
>
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
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> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
--
/Regards,/
Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Singapore
Tel: 6316-2884
/
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