[gmx-users] minimized on protein-protein decoys

Liu Shiyong liushiyong at gmail.com
Sun Mar 9 07:07:40 CET 2008

Hi,  all

My purpose is to get the binding energy by gromacs.
I tried to minimize protein-protein docking decoy by using gromacs without
water. But after being minimized, the ligand ran away from receptor.

That's not what I expected . I just want to relax the protein-protein
interface due to some atom-atom contact crash .

By the way, I found the net charge is not zero after adding H atoms on
complex by pdb2gmx.  Can I solve the non-zero net charge problem by adding H
atom on receptor and ligand


Any tip is appreciated.


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