VMD-L Mailing List

From: Marzieh Dehghan (M_Dehghan_at_ibb.ut.ac.ir)
Date: Wed Sep 25 2013 - 07:30:05 CDT

Hi every body

I want to do protein-ligand docking by autodock4, this protein must be
glycate at residue 50, so in order to determine box dimensions and X, Y,Z
center, I used the following scripts by VMD:

set sel [atomselect top "same residue as (within 6 of resid 50)"]
measure center $sel

set a [measure minmax $sel]
vecsub [lindex $a 1] [lindex $a 0]

I have two problems:

1- after finishing docking, according to the best energy level, glucose has
been bonded to residue 48 and 46. I would like to know what script can I use
that glucose is bonded to protein at residue 50?
2- I set number of GA runs on 250 but this docking has automatically been
finished on 140, please guide me?

best regards

Dehghan