VMD-L Mailing List

From: pragya.saxena_at_research.iiit.ac.in
Date: Tue Jan 04 2011 - 04:51:39 CST

Hi,

I am using fitframes.tcl to write a dcd file for only protein (Dihydrofolate reductase-methotrexate---DHFR-MTX).

## This takes a selection and fits that selection for every frame in the
## molecule (all atoms are moved, but the fit is based on the selection).
##
## For example: fitframes top "protein"
##
## -Jim
set molid top
set seltext protein
mol load pdb ionized.pdb dcd md03_traj.dcd
  set ref [atomselect $molid $seltext frame 1]
  set sel [atomselect $molid $seltext]
  set all [atomselect $molid all]
  set n [molinfo $molid get numframes]
  set fin [expr $n-1]
   
  for { set i 1 } { $i < $n } { incr i } {
    $sel frame $i
    $all frame $i
    $all move [measure fit $sel $ref]
  }
animate write dcd fitted_all2.dcd beg 1 end $fin waitfor all sel [atomselect top protein]

However in the resultant dcd file, the cordinates for drug(MTX) are also coming..
Following is the drug in the pdb file that I am using

ATOM 2490 N1 MTX O 161 32.399 40.535 11.719 1.00 0.00 O1 N

I have tried various selections for seltext variable like:-
protein and not resname MTX
protein and not resid 161
protein and not MTX
segid P1 #(for protein)

I want to know where I am going wrong and what should be done.
Kindly help.

Thanks and Regards
Pragya Saxena