[gmx-users] Multiple chains, cofactors and ligands--ffgmx unreliable?
YOLANDA SMALL
yas102 at psu.edu
Fri Feb 3 17:16:51 CET 2006
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
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> >
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
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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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gmx-users at gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-users
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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.
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