VMD-L Mailing List

From: Joaquim Rui de Castro Rodrigues (joaquim.rodrigues_at_ipleiria.pt)
Date: Tue Aug 27 2013 - 10:39:46 CDT

Dear Mohammad,

Check you atom selections.
The selection "segname TMC and chain A" returns 0 atoms on the file that I got from PDB. You may want to select "resname TMC and chain A" instead.
Also, you create two selections, complexA and complexB, that are not used. You are always using $complex in the last two measure commands.
Finally, mind that your selection $complex includes ALL atoms, including water molecules and 2 SO4 ions. You may want to exclude those...

Hope this helps,
Rui Rodrigues

 

________________________________________
De: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] Em Nome De m r [gmstma_rezaei_at_yahoo.com]
Enviado: terça-feira, 27 de Agosto de 2013 14:35
Para: vmd-l_at_ks.uiuc.edu
Assunto: vmd-l: Problem in buried surface area calculation

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