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

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Mar 12 16:00:56 CET 2010

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,


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

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