[gmx-users] Regarding defining termini in new rtp entry

[Joe Joe]

Thank, that did the trick!!!

On Fri, Mar 12, 2010 at 7:00 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> 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 <ilchorny at gmail.com> 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
> >
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
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