[gmx-users] topology for a cyclic peptide

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 26 01:03:13 CEST 2010

Rebeca García Fandiño wrote:
> Hi,
> I am trying to get  the topology of a cyclic peptide, but when I try to 
> do pdb2pgx I get automatically the correction to a terminal one.
> I have looked in the Gromacs list and I only have found a entry about 
> it,  http://osdir.com/ml/science.biology.gromacs.user/2006-08/msg00297.html
> but I cannot find a solution from there.
> Does anyone have any idea about it, please?

You'll have to do a bit of manual work yourself.  I don't entirely understand 
the approach quoted above, but running pdb2gxm -ter (choosing "None" for both 
termini), then adding all necessary bonded information (bonds, angles, 
dihedrals, and impropers) manually should do the trick.


> Thanks a lot for your help.
> Best wishes,
> Rebeca García
> Santiago de Compostela University
> Spain
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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