VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 27 2013 - 10:33:21 CDT

Hi,
  In order to check your work, we would need a copy of the input files
as well as the steps you listed below to ensure that all of the atom
selections you used were correct. For now, I would suggest that you
visualize the selections you're using to ensure that you are indeed
asking VMD to compute what you think you are, and that there are no
errors in the selections themselves...

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 27, 2013 at 06:35:55AM -0700, m r wrote:
> Dear all,
> I'm calculating the buried surface area for the complex 1E2K.pdb.
> It's composed of chains A and B, with a copy of the ligand "TMC"
> bound to each of the chains. However, TMC bound to chain A is
> completely covered by the protein, while TMC bound to chain B is
> partially accessible by solvent.
> To check this in VMD, I used the following commands:
> mol new 1E2K.pdb
> set complex [atomselect top "all"]
> set n 500
> set prA [atomselect top "protein and chain A"]
> expr {([measure sasa 1.4 $complex -restrict $prA -samples $n])}
> 7869.8974609375
> set prB [atomselect top "protein and chain B"]
> expr {([measure sasa 1.4 $complex -restrict $prB -samples $n])}
> 8787.044921875
> set TMCa [atomselect top "segname TMC and chain A"]
> set complexA [atomselect top "(protein and chain A) or (segname TMC and
> chain A)"]
> expr {([measure sasa 1.4 $complex -restrict $TMCa -samples $n])}
> 0.0
> set TMCb [atomselect top "segname TMC and chain B"]
> set complexB [atomselect top "(protein and chain B) or (segname TMC and
> chain B)"]
> expr {([measure sasa 1.4 $complex -restrict $TMCb -samples $n])}
> 0.0
> The last result is obviously wrong, as the ligand "TMC" is partially bound
> and
> accessible by solvent. Due to this result (i.e. zero ASA for the ligand),
> I didn't continue to calculate the buried surface area from the following
> equation:
> [SASA(prB) + SASA(TMCb)] - SASA(complexB)
> I appreciate if anyone could point out why the last result (for TMCb) is
> wrong
> and how to deal with it.
> regards,
> Mohammad 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/