VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 17 2009 - 11:35:58 CDT

Hi,
  From the look of it, you're aligning only the protein backbone
atoms and nothing else. The "$sel move" isn't moving the non-backbone
atoms. I have no idea what your structure looks like, but I think this
is a cause for concern. I would have expected you to apply the resulting
alignment transformation to the entire protein, not just the backbone
atoms that you used to determine the alignment transformation. If this
is creating problems, I would expect you might be able to see it visually
before you calculate the averaged positions and launch the calculations
with the NAMDEnergy tool. Perhaps others can comment further, I can't
say much mor since I have no idea what your structures look like at
each step of your calculation.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Sep 17, 2009 at 05:03:36AM +0000, Andres Morales N wrote:
> Dear user:
>
>
> I am studing protein conformational substates, I need to get the average
> structure from clsters of structures, I use the following script to do
> that:
>
> set ref [atomselect top "protein and backbone" frame 0]
> set nf [molinfo top get numframes]
> set sel [atomselect top "protein and backbone"]
>
> #align
>
> for {set i 0 } {$i < $nf } { incr i } {
> $sel frame $i
> $sel move [measure fit $sel $ref]
> $sel1 frame $i
> }
> # calculate average structure
>
> set sel1 [atomselect top all]
> set nf [molinfo top get numframes]
> set n [expr $nf - 1]
> set newpos [measure avpos $sel1 first 0 last $n step 1]
> $sel1 set {x y z} $newpos
> $sel1 writepdb "promedio.pdb"
>
>
> I need to calculate energy of each average structure. I used NAMDEnergy
> tool to do it. So the results were not good. For example, I have a cluster
> of eleven structures (frames) which energy is between -1100 and -1000
> kcal/mol (calculated with NAMDEnergy too); but average structure's energy
> is 15094 kcal/mol. I do know what is wrong. I wait somebody can help me.
>
>
> Thanks for your suggestions.
>
>
> Andres
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078