[gmx-users] SAS for membrane protein

[Justin Lemkul]

On 5/24/16 8:43 AM, Maximilien LOPES RODRIGUES wrote:
> 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.
>

The calculation group is protein + membrane, then choose just the protein for 
output.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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