[gmx-users] how to include Fe-S topology in .rtp file

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 8 13:19:45 CEST 2009

amri ta wrote:
> hi all...
> I am simulating a protein with Fe-S cluster. What is the protocol for 
> generating a .rtp file with Fe-S topology...As i am using ffG43a1 
> forcefield.. i searched FFG43a1bon.itp file for Fe-S bond, angle and 
> dihedral type... but it is not there..what i should do?..
> If anyone have the idea of the procedure..please outline me the procedure..

Then the exceptionally difficult task of parameterization falls to you.  Running 
a simulation with an Fe-S cluster will require very advanced knowledge of 
Gromacs and the force field for which you are designing the parameters.  Take 
special note of the information here:



> Thanks..
> Amrita
> Ph.D scholar,
> Burdwan University.
> ------------------------------------------------------------------------
> Cricket on your mind? Visit the ultimate cricket website. Enter now! 
> <http://in.rd.yahoo.com/tagline_cricket_1/*http://beta.cricket.yahoo.com>
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list