CCL: Looking for ways of RMSD calculation on different docking
softwares
- From: "Atul Agarwal" <aagarwal *
achillion.com>
- Subject: CCL: Looking for ways of RMSD calculation on different
docking softwares
- Date: Mon, 7 May 2007 09:52:35 -0400
Sobia,
Attached herein is the solution from CCG tech support.
Cheers,
Atul Agarwal
Achillion Pharm
300 George St
New Haven, CT 06511
-----Original Message-----
> From: owner-chemistry a ccl.net [mailto:owner-chemistry a
ccl.net]
Sent: Monday, May 07, 2007 4:06 AM
To: Atul Agarwal
Subject: CCL: Looking for ways of RMSD calculation on different docking
softwares
Sent to CCL by: "Sobia Ahsan Halim" [sobia_halim###yahoo.com]
Dear All
Hi.
I am trying to redock compounds on the protein's active site.But I am
facing so many problems.
(1)I am working on MOE2006.08 and wants to calculate RMSD between the
docked conformation of the ligand and the ligand in the complex
structure of protein but I couldn't find any option to calculate RMSD.
If anyone can tell me the best possible way to calculate RMSD on
MOE2006.08 or SVL and can give me command to calculate RMSD on SVL, I
will be deeply grateful.
(2)I am also working on AutoDock Tools, I find least energy but very
high RMSD or vice versa. What is the possible way to overcome this
problem?.
(3)Is there any posssibility to directly calculate RMSD between two
ligands which are of different vectors on VMD?????....
(4)Is there any option to calculate RMSD on FlexiDock???...
It will be highly appreciated if anyone can help me out..
Thanks in a million.
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Subject: RMSd between two ligands
Date: Mon, 5 Feb 2007 16:03:06 -0400
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Thread-Topic: RMSd between two ligands
Thread-Index: AcdJYJRRt9yNMsmxRQe1ZhLj4yckaw=> From: "Emilio Xavier
Esposito" <emilio a chemcomp.com>
To: <atulagarwal_92128 a yahoo.com>,
"Atul Agarwal" <aagarwal a achillion.com>
This is a multi-part message in MIME format.
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Hi Atul
I've attached an SVL script to calculate the RMSd between two ligand
chains in the MOE 3D window.
*Using rms.svl*
- Save the file 'rms.svl' in your ~/svl directory
- Load the file 'rms.svl' using the MOE Command Window:
svl> load 'rms.svl'
- To calculate the RMS between 2 ligands, in the MOE Commands window type:
svl> rms[]
- The results will be returned to the SVL Command Window
Please feel free to contact me if you have any additional questions
regarding this script or MOE in general.
All the best
Emilio
--
Emilio Xavier Esposito
Applications Scientist
Chemical Computing Group, Inc.
Phone: 514.393.1055
emilio a chemcomp.com
~~~~~~~~~~~~~~~~~~~~~~~
Please join us for the
MOE Workshop in *San Diego*
Wednesday, March 14, 2007
1:00 - 5:00PM
http://www.chemcomp.com/ssupport-workshop.htm
Please make plans to attend the
CCG Users Group Meeting (UGM)
June 26 - 29, 2007
Hotel Godin
Montreal, Canada
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