AW: VMD_waterbox

From: Norman Geist (
Date: Mon Sep 17 2012 - 02:18:29 CDT



you cannot use VMD to setup a amber system. The VMD internal build tools
only work for charmm. You have to use xleap/tleap.


Norman Geist.


Von: [] Im Auftrag
von Shomesankar Bhunia
Gesendet: Montag, 17. September 2012 08:48
Betreff: namd-l: VMD_waterbox



 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.

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