[gmx-users] getting started with gromacs
kumud0405 at gmail.com
Tue Jan 24 17:23:45 CET 2012
I want to do energy minimization of a small peptide (19 residues long) file
(in pdb format).
Can you please tell which tutorial is best for this purpose and which force
field should I use.
On Tue, Jan 24, 2012 at 10:43 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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 tutorial you're looking at is outdated.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 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
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