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 <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*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
========================================
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