[gmx-users] Multiple chains, cofactors and ligands

[Daniela S. Mueller]

hi yolanda,

don't know if this is the solution, but you might check it:
in the molecules section at the end of the topology file, the molecules 
have to be listed in the same order as they occur in the structure file.

hope this helps...

daniela


YOLANDA SMALL wrote:
> 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

-- 

Daniela S. Mueller

Diplom biologist
______________________________________________________________________

-Molecular Dynamics Group, UQ -

Address:
School of Molecular and Microbial Sciences (SMMS)
Chemistry Building (#68)
University of Queensland
Qld 4072, Brisbane
Australia

Phone: +61-7-33653732
Email: d.s.mueller at uq.edu.au

Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm

**********************************************************************

- MD group, RuG -

Address:
Molecular Dynamics
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands

Email: d.s.mueller at rug.nl

Website: http://www.rug.nl/gbb/md
______________________________________________________________________