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: domm...@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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