[gmx-users] minimized on protein-protein decoys

Mark Abraham 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 
water interactions.

> I tried to minimize protein-protein docking decoy by using gromacs 
> without water. But after being minimized, the ligand ran away from 
> receptor.

"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
> separately?

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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