[gmx-users] Joining two peptide chains

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Apr 9 10:14:28 CEST 2010

Hi Anirban,

If you have the two chains in one file, with identical chain
identifiers and no TER statement in case it's a PDB file, then running
pdb2gmx will actually create the bond between them (no matter how far
away the termini are).



On Fri, Apr 9, 2010 at 9:37 AM, Anirban Ghosh
<reach.anirban.ghosh at gmail.com> wrote:
> Hi ALL,
> Is there any way in GROMACS to join two peptide chains by forming a peptide
> bond between the C and N atoms?
> Any suggestion is welcome.
> Regards,
> Anirban
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

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