Hi Hinge, pdb2gmx is intended to convert protein/nucleic acid chains into topologies. It's not a magical program to convert whatever compound into a topology. Just what it says, there's no residue COA in the database for the force field you're trying to use. Check another force field or try to find parameters in literature or on the web (but do mind to check them!).
Cheers, Tsjerk On Dec 30, 2007 10:21 AM, vijay kumar hinge vijay <[EMAIL PROTECTED]> wrote: > Hello users, > > iam using gromacs 3.3 version on linux platform.my protein contain 86 > residues and ligand molecule (palmityl coA) > i got the error while running pdb2gmx with force field gromacs96 43a1.itis > saying that > Fatal error: > Residue 'COA' not found in residue topology database > i wil be very thank full to you if any one can give the sugesstion > ------------------ > HINGE VIJAYA KUMAR > SUN-CoE in Medical Bioinformatics > EMBnet INDIA node > Centre for DNA Fingerprinting and Diagnostics (CDFD), > Gundipet, Hyderabad > INDIA-500 076 > > Ph.No : +91-40-27151344 > ------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
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