From: Akshay Patny (
Date: Thu Sep 21 2006 - 10:18:10 CDT

Dear All


I am trying to solvate my POPC Bilayer generated by VMD on both sides using
the solvate plug-in. I am using the following command from the CTBP workshop
by Dr. Richard Law


solvate protein_and_membrane.psf protein_and_membrane.pdb -b 3.3 -z 5 +z 5
-o solvated


Here the value of -b variable is set to 3.3 (which corresponds to minimum
distance between water and solute). The default value is however given to be
2.4 Angstroms.


Can someone suggest me, based on what criteria should we vary this, or
whether the default value will be good for the Bilayer solvation on both


Thanks in advance for suggestions.





Akshay Patny

Graduate Research Assistant
Faser Hall 417, Department of Medicinal Chemistry

Research Institute of Pharmaceutical Sciences
University of Mississippi
University, MS 38677
Tel: 662-915-1286 (office); Web: