[gmx-users] query for g_sas

Dilraj Lama dennis at iitk.ac.in
Thu Mar 6 20:12:46 CET 2008

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.

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.

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

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