[gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue 50

Justin Lemkul jalemkul at vt.edu
Sun Jan 14 16:55:32 CET 2018

On 1/14/18 10:52 AM, ABEL Stephane wrote:
> Thanks Justin
> First I forgot to say that I am building a cyclic peptide (Atosiban, https://fr.wikipedia.org/wiki/Atosiban). I construct two RTP for the  MER (3-Mercaptopropionyl-) and TYO (ethoxy tyrosine. And they are correct since the two residues are well constructed and linked together with pdb2gmx as it is shown If I consider the ILE as NILE
> For linking the MER and CYX I define a bond with the specbond.dat (the corresponding bond is shown in the  pdb2gmx output). The only problem I have is that NILE residue is chosen instead of ILE
> How to resolve this problem and to force pdb2gmx to use ILE ? It is strange or I found a subtle error I cannot find.

I've never dealt with cyclic peptides in GROMACS and most threads about 
them tend to die off without resolution. It's not something pdb2gmx does 
well. Presumably you could use the -missing flat (very dangerous!) and 
then verify that the topology has all the special bonds it needs.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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