VMD-L Mailing List

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Wed Apr 11 2007 - 21:42:25 CDT

Dear users,

Can one reproduce dssp ACC value using "measure sasa"?

What are the atom radii in VMD?
same as dssp's? (1.4 for O, 1.65 for N, 1.87 for Ca, 1.76 for C of CO
in the backbone,
1.8 for all sidechain atoms, and 1.4 for water)
If I load a trajectory with Amber topology, then do I use amber atom radii?

Is "srad" solvent radius like 1.4 for water in dssp?

I compared dssp and vmd using the same pdb file (X-ray structure from PDB).
I've got much larger asas values using VMD than those using dssp program.
I think the difference is not from small differences of atom radii.

Since dssp report every residue ACC value, I used the following

set sel [atomselect top "resid 11 and chain A"]
measure sasa 1.4 $sel

Even when I selected only sidechain, I got large value.

Any comment will be appreciated. 

-- 
Best wishes,
MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
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Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi