VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri May 30 2008 - 07:49:45 CDT

On Fri, 30 May 2008, andrea spitaleri wrote:

AS> }
AS>
AS> # now loop and compare
AS> for {set i 0} {$i < $nrmols} {incr i} {
AS> set trans_mat [measure fit $sel($i) $sel(0)]
AS> set all [atomselect $i all]

i would say the error is here. the molecule don't start
from 0. you have to use $mid($i) instead of $i.

axel.

AS> $all move $trans_mat
AS> set rmsd [measure rmsd $lig($i) $lig(0)]
AS> set my [lindex $data $i]
AS> set nrmsd [format %.3f $rmsd]
AS> puts $outfile " $my $nrmsd"
AS> }
AS> # now clean up
AS> for {set i 0} {$i < $nrmols} {incr i} {
AS> set sel($i) delete
AS> set lig($i) delete
AS> mol delete mid($i)
AS> }
AS> close $outfile
AS> }
AS>
AS> thanks in advance for any help,
AS>
AS> regards,
AS>
AS> Andrea-
AS>
AS>
AS>
AS> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.