[gmx-users] Error in PDB2GMX

[Justin A. Lemkul]

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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