[gmx-users] Re: Help on gromacs

David van der Spoel spoel at xray.bmc.uu.se
Sat Mar 12 15:05:20 CET 2005

On Fri, 2005-03-11 at 20:24 +0530, Ranjit Kumar wrote:
> Hi,
> I am a reserach student working on MD of a protein-ligand complex.I
> got your id from the mailing list of gromacs.I want to study molecular
> dynamics of protien-ligand complex(pdbid 1yet).I created the topology file
> for ligand from the PRODRG server.when i run the grompp script it gives
> error as Atom TYPE not found for three-four atom types(OS,CR61,CB etc).I
> think you also
> have same problems.I am using the latest version of gromacs on linux.Can 
> you tell me the process to solve the problems?
You're probably mixing force fields.
prodrg supports gromos87 and maybe gromos43a1

> Waiting for the reply....
> Ranjit Kumar
> Indian Institute of Science
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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