[gmx-users] Multiple chains, cofactors and ligands--ffgmx unreliable?

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Feb 3 23:00:02 CET 2006


Hi Yolanda,

That is a bit of a matter of taste or believe, but probably Yang Ye is
correct that OPLS is among the best choices. However, the Gromos force
fields have proven their value too. The problem with the gmx force field is
that the development has stopped some while ago, it was sort of abandoned,
and it doesn't always give the 'right' behaviour. This has crossed the
mailing list in the past several times. For specific information, other
people will prove more useful...

Cheers,

Tsjerk

On 2/3/06, Yang Ye <leafyoung81-group at yahoo.com> wrote:
>
> 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
> >>> Please don't post (un)subscribe requests to the list. Use the
> >>> www interface or send it to gmx-users-request at gromacs.org.
> >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>>
> >>>
> >>> _______________________________________________
> >>> 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.
> >>> Can't post? Read 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 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
> >
> >
> >> gmx-users at gromacs
> .orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease
> >>
> > don't post (un)subscribe requests to the list. Use thewww interface or
> send it
> > to
> >
> >> gmx-users-request at gromacs.org.Can't post? Read
> >>
> > http://www.gromacs.org/mailing_lists/users.php
> >
> >> _______________________________________________gmx-users mailing list
> >>
> > gmx-users at gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-users
> >
> >> Please don't post (un)subscribe requests to the list. Use thewww
> interface or
> >>
> > send it to gmx-users-request at gromacs.org.Can't post? Read
> >
> >> 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
> > www interface or send it to gmx-users-request at gromacs.org.
> > 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
> /
> _______________________________________________
> 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.
> Can't post? Read 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 Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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