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From: madhumita das (madhumita.bioinfo_at_gmail.com)
Date: Wed Sep 07 2011 - 20:24:47 CDT

---------- Forwarded message ----------
From: madhumita das <madhumita.bioinfo_at_gmail.com>
Date: Wed, Sep 7, 2011 at 10:19 PM
Subject: Pdb file generation,bad water removal and coordinates of psf.
To: owner-vmd-l_at_mailhost.ks.uiuc.edu

Hi,

      I have generated a membrane protein complex and then added a waterbox
using Gromacs,but instead of being at the outer surfaces of lipid
membrane,water spreads all around the membrane,I tried to use vmd to remove
bad water,for this I used tcl scripts to split pdb and generate psf
files,but I couldn't find the appropriate commands to generate pdb file for
lipid molecule as well as whenever I try to generate psf files from the
obtained pdb file for water,it becomes fail to generate coordinates.

                               Please help me.

      Thanks

       Madhumita Das