[gmx-users] Cyclic Peptide Topology

jriedel jan.riedel at tu-dortmund.de
Mon Jul 15 01:07:38 CEST 2013


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
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:
>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

View this message in context: http://gromacs.5086.x6.nabble.com/Cyclic-Peptide-Topology-tp5009832.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list