On 2/12/18 3:09 PM, farial tavakoli wrote:

First, please note that this line is not doing anything:
define        =  -DUSE_OLD_C3

If you're trying to use the old CHARMM36 parameters, and not CHARMM36m, the correct keyword is -DUSE_OLD_C36. We only included that in the case that people wanted to do force field comparisons, because for folded proteins, C36 and C36m are almost identical by virtue of how we did the reparametrization.

but when I checked nvt.gro by VMD ,  viewed  the receptor and ligand went out 
of the box, almost completely and ligand was separated from the protein, 
completely. Is there anyone who can help me and advice me why it was happened?

Sounds like a typical PBC imaging issue. Just use trjconv.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129


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