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
--
========================================
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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