Please keep all Gromacs-related correspondence on the gmx-users list. As I have
said dozens of times, I do not advertise myself as a private tutor, nor do I
always have the right solutions.
sunny mishra wrote:
Dear Justin,
I read your solutions always in the GROMACS discussion topics. I have
also got one problem this time while using pdb2gmx. I am working on
HIV-1 Protease with PDB ID 1A8G.pdb. I am trying to convert this
protein structure to COARSE GRAINED protein structure and I am done
with that but when I am trying to make the topology and conf.gro file
from my CG structure of 1A8G.pdb using pdb2gmx it gives me the FATAL
ERROR something like this.
FATAL ERROR : Incomplete Ring in HIS 69.
Which CG model are you using? The one most commonly used with Gromacs is
MARTINI, and its setup procedure does not require the use of pdb2gmx; the
authors make scripts available that generate your topology for you.
-Justin
Now, I am really confused that what will be the solution of this
thing. I am also new to GROMACS and I have no idea about the solution
of this problem. I would highly appreciate your help for the same.
Thanks,
Sunny Mishra
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
