From owner-chemistry@ccl.net Mon May  7 11:38:00 2007
From: "Atul Agarwal aagarwal##achillion.com" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL: Looking for ways of RMSD calculation on different docking softwares
Message-Id: <-34205-070507113713-10149-GrLzU+N0/v4gWg7BmapThQ- -server.ccl.net>
X-Original-From: "Atul Agarwal" <aagarwal===achillion.com>
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Date: Mon, 7 May 2007 11:36:18 -0400
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Sent to CCL by: "Atul Agarwal" [aagarwal(_)achillion.com]
Sobia:

Looks like the attachment did not go through.  Here it is:

#svl
//	rms.svl		calculates the RMS between two chains (and only
two)
//
//	01-feb-2003 (exe) Created
//
// COPYRIGHT (C) 1998-2007 CHEMICAL COMPUTING GROUP INC.  ALL RIGHTS
RESERVED.
//
// PERMISSION TO USE, COPY, MODIFY AND DISTRIBUTE THIS SOFTWARE IS
HEREBY
// GRANTED PROVIDED THAT: (1) UNMODIFIED OR FUNCTIONALLY EQUIVALENT CODE
// DERIVED FROM THIS SOFTWARE MUST CONTAIN THIS NOTICE; (2) ALL CODE
DERIVED
// FROM THIS SOFTWARE MUST ACKNOWLEDGE THE AUTHOR(S) AND INSTITUTION(S);
(3)
// THE NAMES OF THE AUTHOR(S) AND INSTITUTION(S) NOT BE USED IN
ADVERTISING
// OR PUBLICITY PERTAINING TO THE DISTRIBUTION OF THE SOFTWARE WITHOUT
// SPECIFIC, WRITTEN PRIOR PERMISSION; (4) ALL CODE DERIVED FROM THIS
SOFTWARE
// BE EXECUTED WITH THE MOLECULAR OPERATING ENVIRONMENT (MOE) LICENSED
> FROM
// CHEMICAL COMPUTING GROUP INC.
//
// CHEMICAL COMPUTING GROUP INC. DISCLAIMS ALL WARRANTIES WITH REGARD TO
THIS
// SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
FITNESS,
// AND IN NO EVENT SHALL CHEMICAL COMPUTING GROUP INC. BE LIABLE FOR ANY
// SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER
// RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF
// CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN
// CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
//
/*

Description:
Calulate the RMS between two chains.  Typical use is for comparing two
ligand chains.

Using:
- 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 chains, in the MOE Commands window
type:
 svl> rms[]

*/


#set title	'RMS Difference'
#set main	'MOE_RMS'

global function rms []
    local atom_keys, num_atoms, chains;
    local num_atoms1, num_atoms2;
    local lig1, lig1_ak, hlig1_ak, pos1;
    local lig2, lig2_ak, hlig2_ak, pos2;
    local rms;

    atom_keys = Atoms[];
    num_atoms = nAtoms[];
    chains = Chains[];

    lig1 = chains(1);
    lig2 = chains(2);

    lig1_ak = cat cAtoms lig1;
    lig2_ak = cat cAtoms lig2;

    hlig1_ak = lig1_ak | aAtomicNumber lig1_ak > 1;
    hlig2_ak = lig2_ak | aAtomicNumber lig2_ak > 1;

    num_atoms1 = length hlig1_ak;
    num_atoms2 = length hlig2_ak;

    write[' Total number of atoms in each ligand = {}\n', (num_atoms/2)
];
    write[' Number of heavy atoms in each ligand = {}\n', num_atoms1 ];

    pos1 = aPos hlig1_ak;
    pos2 = aPos hlig2_ak;

//    write['Positions of Atoms = {}\n',pos1];
//    write['Positions of Atoms = {}\n',pos2];

    rms = sqrt ((add (sqr (pos1(1) - pos2(1)) + sqr(pos1(2) - pos2(2))
                + sqr(pos1(3) - pos2(3)))) / num_atoms1) ;

    write['RMSd = {}\n',rms];

endfunction


*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

Atul

-----Original Message-----
> From: owner-chemistry[*]ccl.net [mailto:owner-chemistry[*]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.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt