Hi Ilya, If it is an amino acid, albeit modified, you can make pdb2gmx recognize it as such by adding it to the file 'aminoacids.dat'. This file is in the installation directory. You can also copy it to your working directory and change it there, as it will then take precedence over the other one. Do mind to increment the number at the top of the file for every amino acid you add.
Hope it helps, Tsjerk On Fri, Mar 12, 2010 at 3:56 PM, Joe Joe <[email protected]> wrote: > How do I tell pdb2gmx what the termini are in my molecule. I added a non > standard amino acid to the ffoplsaa.rtp database but pdb2gmx says "No N- or > C-terminus found: this chain appears to contain no protein". > thanks, > Ilya > > -- > gmx-users mailing list [email protected] > http://lists.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. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list [email protected] http://lists.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
