sunny mishra wrote:
Thats great. I am able to make now my 1A8G.itp file and also the CG
structure of protein but now the other problem which is arising is to
make the topol.top file and conf.gro file. When I am making this using
the command...pdb2gmx -v -f 1A8G_CG.pdb -o conf.gro -p topol.top
......it says choose the forcefield parameter and I am choosing OPLS
rather as a matter of fact I have tried all force field parameters and
when I run it says FATAL ERROR : Incomplete ring for HIS 69.
Do not use pdb2gmx. I have told you that twice. Follow the tutorial on the
MARTINI site:
http://md.chem.rug.nl/~marrink/MARTINI/Downloads/Tutorial/tutorial.pdf
The necessary files are available for download at:
http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html
-Justin
Don't know how to proceed.
Thanks,
Sunny
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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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