VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 12 2007 - 15:08:32 CDT

Hi,
  Yes, what you've got there looks correct for the use of the
VMD 'measure sasa' command. If you want to make sure that
you're calculating the accessible surface area for the right
part of your structure you can use the -points flag to store the
samples into a variable and feed them into VMD draw commands to
visually inspect the resulting sample points. That can also be
handy if you need to avoid internal pockets or voids and aren't sure
if they're affecting the result. I can't say anything regarding
the DSSP SASA method since I'm not personally familiar with it
at this time.

  John Stone
  vmd_at_ks.uiuc.edu
 
On Thu, Apr 12, 2007 at 11:02:14AM -0400, Myunggi Yi wrote:
> 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 

-- 
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