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

From: Edward Patrick Obrien (edobrien_at_Glue.umd.edu)
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
script.

Regards,
Ed

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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