[gmx-users] Cyclic Peptide Topology

[jriedel]

Hi,

I'm want to run a MD simulation with a Phe-Phe-Phe-Phe-Gly cyclic peptide.
But I'm have problems generating the topology files. When I try to use the
strategy to generate a topology file for the linear FFFFGF
using
pdb2gmx -ff charmm27 -f pep.pdb -o pep.gro -ter -water spce
and choosing None for both termini
I will get the following error
>-------------------------------------------------------
>Program pdb2gmx, VERSION 4.6.3
>Source code file: /home/johnny/gromacs-4.6.3/src/kernel/pdb2top.c, line:
110
>
>Fatal error:
>There is a dangling bond at at least one of the terminal ends. Fix your
coorate file, add a new >terminal database entry (.tdb), or select the
proper exing terminal entry.
>For more information and tips for troubleshooting, please check the GROMACS
>website at http://www.gromacs.org/Documentation/Errors
>-------------------------------------------------------


Has anybody an idea how i can overcome this problem or some kind of tutorial
to generate the topologies files for a cyclic peptide ?

Thanks in advance
Cheers
Jan



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