[gmx-users] SAS for membrane protein

[Maximilien LOPES RODRIGUES]

Hi dear gromacs users,

It's the first time I use this mail list, I hope it will work fine.

I have simulated a membrane protein in a lipid bilayer with water etc. Everything is fine but I now want to calculate the accessible surface of the protein. Can you help me to understand how does it work ?

I obviously have a .gro (or .pdb) containing the system and an index file to select only the protein, lipids,...
"gmx sasa" is the command to use. But I don't know how to only calculate the SAS of the part of the protein that is effectively in contact with water ? I mean, we have to exclude the hydrophobic surface that is in contact with lipids.

Is my question understandable ?

Thank you in advance. Hope I can help in return.
Kind regards,
Max
-- 
Maximilien LOPES RODRIGUES
PhD student 

Département de Chimie
Chimie-Physique des Biomolécules (CPB)

Tel. +32 (0)81 72 45 23
Fax. +32 (0)81 72 45 46

maximilien.lopesrodrigues at unamur.be
https://directory.unamur.be/staff/mlopesro

Université de Namur
Rue de Bruxelles 61 - 5000 Namur
Belgique