[gmx-users] problem with FeS cluster

[Justin A. Lemkul]

subarna thakur wrote:
> Hi
> I have gone through the material you have earlier mentioned but  I am 
> still in dark and not sure where to start. Should I make chages in the 
> relevent .rtp file to incorporate the atoms of the FE-S cluster?

If you derive your own parameters, you can either make an .rtp entry for the 
cluster, or simply generate an .itp file by hand.  Either way will work, but no 
matter what, it is not a trivial task to derive the appropriate parameters. 
Making and .rtp entry/.itp file is simple, proving the validity of your 
parameters is not.

-Justin

> Subarna
> 
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Wednesday, 3 June, 2009 4:46:37 PM
> *Subject:* Re: [gmx-users] problem with FeS cluster
> 
> 
> 
> subarna thakur wrote:
>  > Hello user
>  > Can anybody please tell me how to prepare a topology file for the 
> FES4 cluster incorporated in a protein
>  > 
> 
> I passed along some useful information to you yesterday.  There is no 
> easy answer.  To do so would involve a large amount of work, in any 
> case, if it is even possible to model this species using a standard MM 
> force field.
> 
> -Justin
> 
>  > Subarna
>  >
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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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-- 
========================================

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

========================================