sunny mishra wrote:
Hi,
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.
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.
Visit the MARTINI site. They have scripts that generate CG protein topologies.
For MARTINI, pdb2gmx is not necessary.
-Justin
Thanks,
Sunny Mishra
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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