[gmx-users] query for g_sas

[Xavier Periole]

On Fri, 7 Mar 2008 00:42:46 +0530 (IST)
  "Dilraj Lama" <dennis at iitk.ac.in> wrote:
> Hello gmx users,
>                I suppose this is one of the more common subject post
> going around in the mailing list. I have gone through the
> list and have gathered some information on the subject.
> But I have some queries and if someone can shed light on
> it, it will be of great help to me.
> 
>                 I am presently trying to calculate the sasa for specific
> residues as a function of time from my simulation
> trajectory.I am using g_sas tool from gromacs ver3.3 for
> the purpose.I wanted to check the values it generated. So
> I created a "gly-X-gly" tripeptide in an extended
> conformation and calculated the "sasa" for the twenty
> amino acids.I also calculated the same using the tool
> "naccess".I then compared the two values with the value
> reported earlier for the various amino acids (J. Mol.
> Biol.196:641-656(1987))
> 
> Values for some of the amino acids are as:
> 
> 	jmb	Gromacs3.3	Naccess
> Ala	113	100	         115
> Arg	241	211	         246
> Asn	158	133	         155
> Asp	151	132	         151
> Cys	140	121	         140
> 
> It seems the values from "naccess" and "jmb(reported in J. Mol. Biol)" are
> similar.I suppose one of the factor for the difference in values between
> "naccess" and "gromacs3.3" could be because of the  "different VDW radii"
> used for the atoms. Naccess uses "Chothia's VDW radii" whereas Gromacs3.3
> uses the VDW radii as reported in gmx_sas.c.

The difference you are seen is due to the use of different methods to
measure the ASA. jmb and naccess use the Richards approach which is based
on the surface defined by the "center" of a probe rolling on the vdW
surface of the solute: the surface uses RvdW+Rsolvent. Gromacs is based on the 
Connolly surface which uses the vdW radius surface and connect them using
a solvent probe: it uses the excluded volume from the solvent.

The Connolly surface must be smaller as it does not include the radius of
the probe in the calculation.

Take a look at the links:
http://www.msg.ucsf.edu/local/programs/moloc/surface.html
http://www.netsci.org/Science/Compchem/feature14e.html

XAvier

> Is it the case?
> 
> Can I go ahead and perform the calculation using this tool?
> 
> I have come accross papers which have used "g_sas" tool for performing the
> "sasa" calculation for the entire protein or peptide. Can anyone refer to
> me some papers where "sasa" calculation has been done for specific
> residues using "g_sas".
> 
> I have also read in the mailing list that differnet versions of Gromacs
> give different "sasa" values.people seem to report that values from
> Ver3.3, ver3.3.1 and ver3.3.2 are different. I haven't used 3.3.1 or
> 3.3.2. So what is the update in this front.Previous people who have gone
> through this, please help me out.
> 
>Finally I also read in the list about the flexibility of chossing the "VDW
> radii" options. Has anything been done yet?
> 
> Thank you.
> -- 
> Dilraj Lama,
> Graduate student,
> Bioinformatics and Biomolecular Simualtion lab,
> Dept. of BSBE;IITK-kanpur,
> Uttar pradesh,India-208016.
> email:dennis at iitk.ac.in,dilraj2002 at yahoo.com
> mob:09415473973
> 
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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------