From: Shaghayegh Vafaei (
Date: Wed Jun 23 2010 - 14:39:53 CDT

Hi all,

I am in the learning stage of Namd and I was wondering if anybody know how to create a pdb file for water from scratch.
I know how separate water pdb from a mix of water-protein pdb.
But I just need a water box pdb. My problem is that I dont know how to make up coordinates .
Even for psf , I couldnt figure out how to define the bond parameters.

I appreciate your help.

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