[gmx-users] getting started with gromacs

[Justin A. Lemkul]

kumud agarwal wrote:
> I tried to use the command pdb2gmx
> 
> *kumud at ubuntu:~/gromacs/gromacs-4.5.5/share/tutor/mciz$  pdb2gmx -ignh 
> -ff G43a1 -f mciz.pdb -o mciz.gro -p mciz.top*
> 
> At the end the message came as
> 
> *Program pdb2gmx, VERSION 4.5.5
> Source code file: pdb2top.c, line: 239
> 
> Fatal error:
> Could not find force field 'G43a1' in current directory, install tree or 
> GMXDATA path.*
> 
> What is the problem here?
> 

The naming of force fields is different in the 4.5.x series.  Whatever tutorial 
you're looking at is outdated.  Try one of the updated ones on the Gromacs 
website, or just choose the force field interactively.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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