Re: Need to add Hydrogens to over 300 distinct PDB's

From: Edward Patrick Obrien (
Date: Wed Aug 11 2004 - 13:05:33 CDT

Hi All,
  I have a solution to my problem of using VMD to automatically guess
atoms for over 300 different PDB files. Thought I'd contribute this
solution in case anyone has a similar problem in the future.

  I've created a perl script that calls VMD to guess atoms and
writes the structure with guessed atoms to file.

  All you need as an input is a list of PDB files you want to guess
coordinates for (and the PDB files themseleves).

  I've attached the script, the directions are in the header of the perl


On Mon, 9 Aug 2004, Edward Patrick Obrien wrote:

> Hi All,
> 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
> atoms.
> Any help would be appreciated,
> Ed

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