GROMACS version: 2021
GROMACS modification: Yes/No
Respected All,
I want to perform MD for cyclic peptide. My question is, how many CMAP values will be there in the topology file of 5 residue cyclic peptide? Is it 4 or 5? (Image attached)
Here I attached the files here, 5 residue peptide along with its topology.
Kindly enlighten me. Thanks in advance.
Hi,
A curiosity: have you used pdb2gmx to build the topology?
From gmx pdb2gmx -h
“gmx pdb2gmx automatically determines if a cyclic molecule is present by evaluating the distance between the terminal
atoms of a given chain. If this distance is greater than the -sb (“Short bond
warning distance”, default 0.05 nm) and less than the -lb (“Long bond warning
distance”, default 0.25 nm) the molecule is considered to be ring closed and
will be processed as such. Please note that this does not detect cyclic bonds
over periodic boundaries.”
\Alessandra
Thank You so much for your reply.
Yes, i used the following command: (topology included in the compressed folder)
gmx pdb2gmx -f 5G.pdb -o 5G.gro -water tip3p -ignh
pdb2gmx made correct bonds, pairs, angles, dihedrals (manually scan the topol.top ) but cmap seems skeptical to me, since i was expecting 5, that made me to raise the above question.
Thanks in advance.
what about your terminals?
None (without NH3+ and COO-)
Same issue here!
I have passed the cyclic decapeptide into the pdb2gmx and the result has 9 CMAP torsions!
I think this issue needs to be reported
Hello,
if you can, please upload a small sample to a new issue on GitLab for this (Issues · GROMACS / GROMACS · GitLab) and tag me (Paul Bauer) there.
I’ll have a look at this.
Cheers
Paul
Thanks. I have opened an issue #4480 there.
This is not a gromacs issue, please check previos reports. In order to make CPN you need to select NON E in terminal patches and also have to edit specbond data. detailed comments are there in previos post. please search "cyclic peptide’ topology.
As far as I know, since GROMACS ver. 2021.1 pdb2gmx can automatically generate topologies for cyclic peptides without supplying terminal patch options. So you do not have to edit specbond.dat file…