[Dock-fans] Metal

Scott Brozell sbrozell at scripps.edu
Tue Sep 25 14:15:53 PDT 2007


Hi,

In addition, for supported elements see
parameters/vdw_AMBER_parm99.defn

For Amber score, see
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-May/001024.html

Scott

On Tue, 25 Sep 2007, Sudipto Mukherjee wrote:

> Hi Snoze,

DOCK6 does support metal atoms. In your case, I guess you want to model the iron in Heme.
Use your favorite modeling software (sybyl or moe are good options) to model Heme as part of the receptor.
Save it as a mol2 file and it should work fine with dock.

Regards
Sudipto Mukherjee
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University
Lab: 631-632-8519, Mobile: 631-220-5744


----- Original Message ----
From: snoze pa <snoze.pa at gmail.com>
To: dock-fans at docking.org
Sent: Monday, September 24, 2007 12:31:59 PM
Subject: [Dock-fans] Metal

How to treat metal in DOCK6.0. Do we have parameter list for different metals
regards
s








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