[gmx-users] Multiple chains, cofactors and ligands

[Tsjerk Wassenaar]

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
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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
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