Thank, that did the trick!!! On Fri, Mar 12, 2010 at 7:00 AM, Tsjerk Wassenaar <[email protected]> wrote:
> 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 >
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