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