[gmx-users] g_sas strange values

[Berk Hess]

>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),=20
>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).=20
>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,=20
>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

Could it be that the small chain in almost buried inside the bigger chain?
g_sas calculates the solvent accessible surface as if the group is 
completely
exposed to the solvent, ie not taking into account that there might be a 
protein
next to it and not solvent. This could explain your results.

If this is the case, you could select both chains in g_sas and look at the 
sas
per residue. Summing the area's of all residues in the small chain should 
then
give the correct result.
The only problem is that the 3.1.4 g_sas does not give correct results for 
the
residue and atom output. I have uploaded a fix for this to the contributions 
page,
but something went wrong so it is not visisble.
You can get the fix at the following link:

http://gromacs.org/contributions/uploaded_contributions/g_sas_fix.tgz

Berk.

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