[gmx-users] Cyclic Peptide Topology

Justin Lemkul jalemkul at vt.edu
Mon Jul 15 01:11:27 CEST 2013

On 7/14/13 7:07 PM, jriedel wrote:
> 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 ?

pdb2gmx is not designed to produce topologies for cyclic peptides.  Check the 
archive for numerous threads on this topic.  Perhaps a specbond.dat entry will 
help, otherwise the sure-fire solution is to manually add the required bonded 
terms (bond, angles, and dihedrals) to the topology after pdb2gmx does its work. 
  The above error can likely be overcome by using -missing (which is OK in this 
instance, but not in many other cases).



Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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