[gmx-users] writing ff parameters as a text file

[Dommert Florian]

On Mon, 2012-04-23 at 12:41 -0400, Justin A. Lemkul wrote: 
> 
> On 4/23/12 11:36 AM, Bala subramanian wrote:
> > Friends,
> > I have created the top (attached) file for a tripeptide using pdb2gmx tool of
> > gromacs. However in the top file, i dnt see the pdb2gmx writing the ff parameters.
> >
> > I guess that the ff parameters are read directly from the ff.itp given in the
> > given as  #include "amber03.ff/forcefield.itp". Is there any way/tool with which
> > i can write these parameters in a separate file.
> >
> 
> You can view forcefield.itp in a text editor, which will show you that it does 
> little more than point you to other files that hold all of the force field 
> parameters, ffbonded.itp and ffnonbonded.itp.  Both of these are also text files 
> that can be viewed very simply.
> 
> -Justin
> 

Hello Bala,

if you want all the interactions defined by the force field and put I
into the top or itp file. You will have to process the output of gmxdump
I think. With the option -sys all bonded and nonbonded parameters are
given.

Cheers,

Flo


> -- 
> ========================================
> 
> 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
> 
> ========================================

-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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