VMD-L Mailing List

From: shgnwgn_at_eden.rutgers.edu
Date: Mon Jun 13 2005 - 09:37:55 CDT

i have a protein crystal which I constructed from individual pdb protein.
The file i'm analyzing contains water molecules from the original pdb
file, which i would like to keep. however, when i run the structure
through psfgen, it will guess some coordinates of hydrogens and delete any
water oxygen it can't measure a coordinate for. only a quarter of the
water molecules or less remain after the hydrogens are added. i can add
hydrogens to it with other programs, but then can not produce a proper psf
file.

i added hydrogens with chem 3d. i then took the pdb file, loaded it into
vmd, selected all, and wrote a psf file in tckon. however the psf file
fails to show which atoms are bonded to each other.

any suggestions on how to make a psf file directly from a pdb file, or
another way to add hydrogen atoms without losing water molecules would be
appreciated.

Ken jordan