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

[Justin A. Lemkul]

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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