[gmx-users] minimized on protein-protein decoys
Mark.Abraham at anu.edu.au
Sun Mar 9 07:41:02 CET 2008
Liu Shiyong wrote:
> Hi, all
> My purpose is to get the binding energy by gromacs.
You can't do this without water. The binding energy involves displacing
> I tried to minimize protein-protein docking decoy by using gromacs
> without water. But after being minimized, the ligand ran away from
"ran away" during what calculation?
> That's not what I expected . I just want to relax the protein-protein
> interface due to some atom-atom contact crash .
That's what position-restrained EM or MD is for.
> 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
Depends what's causing the non-zero charge. Integral non-zero charge is
different from non-integral. Some integral charges are sensible, some
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