[gmx-users] getting started with gromacs

[kumud agarwal]

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?

Thanks
Kumud Agarwal




On Tue, Jan 24, 2012 at 9:38 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> kumud agarwal wrote:
>
>> How can I check if Gromacs is properly installed on my system (ubuntu)?
>>
>>
> http://www.gromacs.org/**Downloads/Installation_**
> Instructions#Getting_access_**to_GROMACS_after_installation<http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation>
>
> Then try any of the commands.
>
> -Justin
>
>  On Tue, Jan 24, 2012 at 9:22 AM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    kumud agarwal wrote:
>>
>>        hi
>>
>>        I am very new to Gromacs.
>>
>>        To start working with Gromacs in which directory do I have to
>>        keep the pdb file that I am working on?
>>
>>
>>    You put files in whichever directory you want to do your work
>>    (provided you have sufficient permission to write in that directory).
>>
>>    -Justin
>>
>>    --     ==============================**__==========
>>
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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