From: Shomesankar Bhunia (
Date: Sun Sep 16 2012 - 23:23:59 CDT

 I want to run a MDS with protein ligand structure. I have generated a
topology+ co-ordinate [prmtop + inpcrd] file for the protein-ligand complex
using antechamber using AMBER GAFF. I have loaded the prmtop file and
inpcrd file for the complex(protein +ligand) in VMD and now i want to add
ions and solvate my protein. When i am trying to solavte it a error message
is displayed "*No psf/pdb, so minmax must be specified*". I calculated the
min max by typing in tk console
set everyone [atomselect top all]
measure minmax $everyone
and i put the values min max but still the error msg is coming. so how to
set the water box and what neccessary files should be generated so that it
can be used in NAMD for molecular dynamics. Thanks in advance.