From: Kamp, Marc vander (Marc.vanderKamp_at_wur.nl)
Date: Tue Aug 10 2004 - 09:46:15 CDT
I would suggest to install a free program (if you don't already have it) such as OpenBabel (http://openbabel.sourceforge.net/) or Vega (http://users.unimi.it/~ddl/vega/) that is capable of adding hydrogens and can be run from the commandline. All you then have to do is use a simple "for" loop in your shell (or shell-script) to issue the hydrogen addition command on all pdb-files.
From: owner-namd-l_at_ks.uiuc.edu on behalf of Edward Patrick Obrien
Sent: Mon 9-8-2004 20:03
Subject: namd-l: Need to add Hydrogens to over 300 distinct PDB's
I have about 300 PDB's that I would like to add hydrogens to, so
obviously I would like to automate the process.
Does anyone have a script (tcl or other) that can loop through a list of
PDB's, add hydrogens and write out the PDB structure with the guessed
Any help would be appreciated,
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