VMD-L Mailing List

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Thu Apr 12 2007 - 10:02:14 CDT

By assigning the radii and selecting the following way,
I can reproduce sasa comparable with dssp.

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

Since the algorithms are different b/w two programs,
I couldn't get the exactly same numbers.

Are these correct?

On 4/11/07, Myunggi Yi <myunggi_at_gmail.com> wrote:
> 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
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi
> 

-- 
Best wishes,
MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306
Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi