[AMBER] optimise ligand geomatry before MD

From: Nitin Sharma <sharmanitin.nus.edu.sg>
Date: Wed, 29 Jan 2014 02:44:53 +0800

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

AMBER mailing list
Received on Tue Jan 28 2014 - 11:00:03 PST
Custom Search