VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Dec 21 2010 - 21:40:43 CST

Indeed, there is a way to do this with a (still undocumented?) order parameter. See Leo's post here: http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/10172.html

On Dec 21, 2010, at 2:38 PM, Lisa Perez wrote:

>
> 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
>>
>>
>>
>