[gmx-users] Fe atom problems....in simulation

[Justin A. Lemkul]

Kamalesh Roy wrote:
> Can you send me the parameters I need to use....for FE....
> 

Most of the force fields in Gromacs have support for Fe built in, at least in 
the context of heme.  What is it that you're trying to do?  If you need new 
parameters for whatever reason, it will be very tricky to do so for a transition 
metal like Fe.  Consider the following:

http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species

-Justin

> 
> On Mon, Apr 16, 2012 at 2:55 PM, francesco oteri 
> <francesco.oteri at gmail.com <mailto:francesco.oteri at gmail.com>> wrote:
> 
>     Hi,
>     You have to had LJ parameters in ffnonbonded.itp file in the
>     subfolder relative to your force-field
> 
>     Francesco
> 
>     Il giorno 16 aprile 2012 11:08, Kamalesh Roy
>     <roy.kamaleshmd at gmail.com <mailto:roy.kamaleshmd at gmail.com>> ha scritto:
> 
>         CAn any one siggest me how can I run simulation a protein
>         containing Fe atom,
>         I have changed the iions.itpfile and included there Fe in
>         residue type.dat
>         bu still it is returning an error.
> 
>         FE parameter not found.
> 
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> 
> 
>     -- 
>     Cordiali saluti, Dr.Oteri Francesco
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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