VMD-L Mailing List

From: Lisa Perez (mouse_at_mail.chem.tamu.edu)
Date: Tue Dec 21 2010 - 14:38:48 CST

I just discovered that it is an ordering problem... Has anyone discovered an "easy way" to get vmd measure fit to use the order you give it instead of numerical order?

Sincerely,

Lisa M. Pérez, Ph.D.

Texas A&M University
Laboratory for Molecular Simulation, Manager
Graduate Faculty
http://lms.chem.tamu.edu/

Department of Chemistry
580 Ross Street
College Station, TX 77842

Chemistry Bldg. RM. 2109
Ofc: (979) 845-9384
Fax: (979) 845-2971

On Dec 21, 2010, at 1:30 PM, Lisa Perez wrote:

>
> I am trying to rmsd a small molecule against a small protein using a subset of 4 atoms and am getting odd results. If I remove all of the 4 atoms of interest from the pdb files and proceed with the rmsd fit, I get expected results but, if the other atoms are present, I get poor results. Here is the small script that I am using to rmsd my 2 molecules (molid 0 is my small molecule and molid 1 is my small protein):
>
> set ref_frame [ atomselect 1 "serial 163 164 141 142" ]
> set other_frame [ atomselect 0 "serial 13 29 6 16" ]
> set trans_matrix [measure fit $other_frame $ref_frame]
> set move_sel [atomselect 0 "all"]
> $move_sel move $trans_matrix
> set rmsdval [measure rmsd $other_frame $ref_frame]
> puts $rmsdval
>
> I have also tried using index instead of serial number. 1 atom overlays perfectly... more than 1 does not.
>
> Any comments and/or help would be greatly appreciated.
>
> Sincerely,
>
> Lisa M. Pérez, Ph.D.
>
> Texas A&M University
> Laboratory for Molecular Simulation, Manager
> Graduate Faculty
> http://lms.chem.tamu.edu/
>
> Department of Chemistry
> 580 Ross Street
> College Station, TX 77842
>
> Chemistry Bldg. RM. 2109
> Ofc: (979) 845-9384
> Fax: (979) 845-2971
>
>
>