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
aren't.
Mark
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