CCL: Looking for ways of RMSD calculation on different docking softwares

 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
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 // 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