[gmx-users] editing parameters

David spoel at xray.bmc.uu.se
Wed May 7 20:12:00 CEST 2003

On Wed, 2003-05-07 at 20:00, Regina R. Monaco, Ph.D. wrote:
> I am setting up a run to do a MD calculation, which includes a ligand 
> (ethidium cation) that pdb2gmx doesn't recognize.  Ethidium doesn't 
> contain any oddly-parameterized atom types.  I have used gaussian to 
> calculate the ethidium charges, but am not sure how to import those 
> charges into the parameter files. Various error messages received while 
> trying to run pdb2gmx have been (depending on force field tried):
> Fatal error: Atom C1 in residue ETH not found in rtp database   **OR**
> Fatal Error: Residue "ET" not found in residue topology database
> as examples.
> What is the procedure for editing the rtp ?
just do it manually Check protein/ligand tutorial at prodrg site,
and modify the topology for your molecule with your charges if you want

> Thanks,
> Regina Monaco
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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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