Dear amber users,
Is it necessary to optimize ligand geometry before molecular dynamics simulation?
I am using AMBER for MD simulation.
I have seen studies where ligand was parameterized according to quantum chemical calculations, which included performing a geometry optimization with Gaussian98
at the Hartree-Fock/6-31G* level before determining atomic charges and atomic types using Antechamber module of the Amber molecular dynamics software package.
However, i have seen studies where ligand were assigned generalized Amber force field (GAFF) atom types and AM1-BCC atomic charges obtained by adding the bond charge correction (BCC) using Antechamber.
Are both protocols comparable ?
As i am thinking to use pose generated as result of docking will the ligand geometry optimization be good idea?
can someone also tell me web-server or software to do ligand geometry optimization for AMBER MD simulation
Thanks and regards,
Nitin Sharma
Department of Pharmacy,Faculty of Science,National University of Singapore,block S7, Level 2, Singapore : sharmanitin.nus.edu.sg<mailto:sharmanitin.nus.edu.sg> ; http://www.linkedin.com/in/imsharmanitin
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Received on Tue Jan 28 2014 - 11:00:03 PST
