[gmx-users] Fes cluster

[Mark Abraham]

subarna thakur wrote:
> Hello 
> The protein I am considering is a homodimer with two chains with a Fe4S4 cluster situated at the interface of two chains with connections with both the chains by cystein residues.I have generated the .itp file of the Fe4S4 cluster and .top of the protein with pdb2gmx command.The .top file is like this-
> -------------------------------------------------------------------------;
> ; File '1braf.top' was generated
> ; By user: root (0)
> ; On host: localhost.localdomain
> ; At date: Mon Jul 27 13:12:40 2009
> ;
> ; This is your topology file
> ; "I Have a Bad Case Of Purple Diarrhea" (Urban Dance Squad)
> ;
> ; Include forcefield parameters
> #include "ffoplsaa.itp"
> ; Include chain topologies
> #include "1braf_A.itp"
> #include "1braf_B.itp"
> ; Include water topology
> #include "spc.itp"
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
> ; Include generic topology for ions
> #include "ions.itp"
> [ system ]
> ; Name
> Protein
> [ molecules ]
> ; Compound #mols
> Protein_A 1
> Protein_B 1
> -------------------------------------------------------------
> I want to know how do I include the Fe4S4 .itp file in the topology file of the protein 

Do you have one? Does your force field have suitable parameters for this 
moiety?

> and How do I include the connect information of the protein and FES cluster.

You will need to understand parts of chapter 5 of the manual thoroughly. 
Work on understanding a simple diglycine .top file first.

Mark