[gmx-users] how to do MD simulation of protein with Fe-S cluster

[Mark Abraham]

amri ta wrote:
> Dear Gromacs users,
> 
>  
> 
> I am currently working on Dynamic simulation studies using GROMACS 
> software. In my current work I want to do simulation of a protein 
> containing Fe-S cluster. If i directly do through pdb2gmx then it is 
> giving a error massage like "FES in not included in .rtp file". 
> Regarding this I went through the Article "Gromacs Tutorial for 
> Drug-Enzyme Complex" which has shown clearly step-by-step how to include 
> new topologies for drug/ligand molecules. But I was not successful in 
> running the dynamics. The "Drug-Enzyme complex" tutorial was specific 
> for ligands/Drugs that do not form part of the protein chain. But if I 
> want to include topology for Fe-S cluster which occur within the protein 
> chain, how to do it?

Firstly you need reliable parameters for your system. Probably none of 
the forcefields included in GROMACS has any, so you will need to search 
the literature to see if any exist. There's sound advice here 
http://wiki.gromacs.org/index.php/Exotic_Species.

Then, if you wish to use pdb2gmx then you'll need to build an .rtp file 
entry for the Fe-S cluster. This is nearly the same as the contents of a 
molecule .itp file. All this stuff is discussed in chapter 5 of the manual.

This kind of simulation is highly unlikely to be suitable for a beginner.

Mark