[gmx-users] g_sas strange values
spoel at xray.bmc.uu.se
Thu Sep 25 19:27:01 CEST 2003
On Thu, 2003-09-25 at 16:06, Andrea Carotti wrote:
> I have a protein composed by two chains (36+247 aa).
> I have tried to use g_sas to calculate the surface only of the light
> chain (36aa),
> so i've crated a group for this residues (365 atoms)and I've got a
> middle value of 125 nm^2(for the total area).
> This value seems to be quite constant during all the simulation.
> I've tried to do the same calculation on some "representative"
> structures with Sybyl and MolMol,
> selecting the same number of residues (and atoms) and I've got a value
> approximatively of 2000 Ang^2.
> I think that this difference is very large. I'm doing something wrong
> with Gromacs?
> I hope someone can help me
Hmm, you didn't say which version of gromacs you used, but apart from
that I have recently compared the current CVS code to the result from
MSMS which uses a different algorithm. The numbers were very close.
There have been some update to the SASA calculation, I don't know
whether they made it into 3.1.4. If not you could try the CVS code.
> Andrea Carotti
> Dip. Farmaco-chimico
> Università di Bari
> via E. Orabona, 4
> CAP 70124
> e-mail : and.carotti at farmchim.uniba.it
> web: http://www.farmchim.uniba.it/samba/
> phone: +39080/5442638
> fax: +39080/5442230
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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