[gmx-users] g_sas strange values

Berk Hess gmx3 at hotmail.com
Fri Sep 26 11:24:01 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),=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

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 
exposed to the solvent, ie not taking into account that there might be a 
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 
per residue. Summing the area's of all residues in the small chain should 
give the correct result.
The only problem is that the 3.1.4 g_sas does not give correct results for 
residue and atom output. I have uploaded a fix for this to the contributions 
but something went wrong so it is not visisble.
You can get the fix at the following link:



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