On Fri, 7 Mar 2008 00:42:46 +0530 (IST)
"Dilraj Lama" <[EMAIL PROTECTED]> 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:[EMAIL PROTECTED],[EMAIL PROTECTED]
mob:09415473973
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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