From owner-chemistry@ccl.net Thu Aug 2 14:01:00 2007 From: "debjani roy\(Chattopadhyay\) debjani_2k2^yahoo.com" To: CCL Subject: CCL: adding hydrogens Message-Id: <-34856-070802121218-5421-CglknIgecFvzZMTVLsr37w],[server.ccl.net> X-Original-From: "debjani roy\(Chattopadhyay\)" Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-2122894649-1186067515=:27457" Date: Thu, 2 Aug 2007 08:11:55 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "debjani roy\(Chattopadhyay\)" [debjani_2k2%a%yahoo.com] --0-2122894649-1186067515=:27457 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi, The program "gwh" ( Amber) sets positions of water hydrogens onto water oxygen positions present in PDB files. It is done by optimizing simple electrostatic interactions (check Amber manual for details). USAGE gwh [-p ] [-w ] [-c] [-e] < input_pdb_file > output_pdb_file Hope this helps, -Debjani --------------------------------------------------------------------------------------------------------------------- "Max Porrini mozz76(0)gmail.com" wrote: Hi all Does anybody know how I can add hydrogens to a system? I've downloaded the pdb file of a enzyme and there aren't hydrogen atoms (for instance the water molecule is formed only by the oxygen). I'd like to saturate my system with the missing hydrogens. Any tips will be very appreciated. thanks a lot MP --------------------------------- Shape Yahoo! in your own image. Join our Network Research Panel today! --0-2122894649-1186067515=:27457 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi,

The program "gwh" ( Amber) sets positions of water hydrogens onto water oxygen positions present in PDB files. It is done by optimizing simple electrostatic interactions (check Amber manual for details).

USAGE

gwh [-p <prmtop>] [-w <water.pdb>] [-c] [-e] < input_pdb_file
> output_pdb_file

Hope this helps,
-Debjani
---------------------------------------------------------------------------------------------------------------------

"Max Porrini mozz76(0)gmail.com" <owner-chemistry|-|ccl.net> wrote:
Hi all
Does anybody know how I can add hydrogens to a system?
I've downloaded the pdb file of a enzyme and there aren't hydrogen atoms
(for instance the water molecule is formed only by the oxygen).
I'd like to saturate my system with the missing hydrogens.
Any tips will be very appreciated.
thanks a lot
MP

Shape Yahoo! in your own image. Join our Network Research Panel today! --0-2122894649-1186067515=:27457--