[gmx-users] Fe+2 not found in forcefield ffG43a1

[Justin A. Lemkul]

Miguel Quiliano Meza wrote:
> Dear Users.
>  
> Maybe this question is easy for all, but i have problems, patience please.
>  

Actually, your situation is quite hard, which is likely why you haven't found a 
solution.

> I do not have experience with metals, now I have a protein (crystal) 
> with Fe+2, which is coordinating with three HISTIDINES, one D and two 
> molecules of water, when I try to run "pdb2gmx" the program tells me 
> "Residue "FE" not found in residue topology database". I opened the 
> database for forcefield ffG43a1 and only found FE for heme group. I 
> search other forcefields for iron+2, but most refer to heme groups. Why? 
> and what happend with Fe+2?
>  

Most likely because the principal motivation for parameterization of 
Fe-containing species revolved around heme.  You've got to be very careful in 
dealing with such systems, for instance:

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

There are numerous reports in the literature of the failings of classical MD 
force fields with respect to metal ions.  At the very least, you'd probably have 
to do some very thorough QM to derive parameters (geometric and otherwise) to 
appropriately represent your system.

Nonbonded parameters are certainly available in ffG43a1 for Fe, just not in the 
context of a pdb2gmx-accessible "residue," so you could, in theory, apply them. 
  Whether or not that is actually appropriate is a different matter altogether.

-Justin

> What can i do? I would very grateful if someone gives advices or ideas.
>  
> thanks in advance
>  
> Miguel
> 

-- 
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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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