[gmx-users] how to do MD simulation of protein with Fe-S cluster
amrita0092002 at yahoo.co.in
Fri May 29 12:07:05 CEST 2009
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.
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