[gmx-users] g_sas strange values

Andrea Carotti and.carotti at farmchim.uniba.it
Thu Sep 25 16:07:01 CEST 2003

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

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
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