[gmx-users] editing parameters

Regina R. Monaco, Ph.D. rocket at earthlight.com
Wed May 7 20:02:00 CEST 2003

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 ?

Regina Monaco

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