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

[amri ta]

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?
 
I tried according to the tutorial but was unsuccessful all the time.
 
I'll be very grateful if you can outline me the procedure to be
followed in such cases.
 
Thank you,
 
Amrita Paul
 


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