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:
http://oldwiki.gromacs.org/index.php/Exotic_Species
-Justin
Thanks..
Amrita
Ph.D scholar,
Burdwan University.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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