Dear Amber users,
I want to calculate protein-protein binding free energy of a homo-dimer. I have the simulations run for it using Amber 12. It does not have any ligand present.
While looking at mmpbsa_pl or mmpbsa_py it seems both of the documentations and examples illustrates calculation of binding free energy for protein-ligand system which includes specifying protein and ligand topology file separately.
Can anybody point me towards the examples of calculating protein-protein binding free energy? or the changes I have to make to use protein-ligand mmpbsa scripts for protein-protein system?
Thanks
Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 01 2013 - 15:30:03 PST
