From: Sindrila Dutta Banik (
Date: Fri Dec 19 2014 - 06:27:01 CST

Dear all,

I want to generate a cubic box of non standard solvent molecule. To
generate this first I generate a pdb file using Molfacture and then
generate psf file from the same. Then edit atom type and partial charge
over in the psf file by vi editor.

Now to generate a box of the solvent molecule using the pdb file of single
molecule I use Tk console but not able to generate corresponding psf file.
If I use the Molfacture it generate a psf file which contains no bond
information. I want to use the previously edited psf file to generate new
box so that the charges and atom type be correct in the new psf file for
the box of solvent. How to do the same; please help me out.

With best regards


Sindrila Dutta Banik
C/O Prof. A. Chandra
Project Scientist
Department of Chemistry
IIT Kanpur
UP 208016