[gmx-users] SAS for membrane protein

[Justin Lemkul]

On 5/24/16 9:35 AM, Maximilien LOPES RODRIGUES wrote:
>> The calculation group is protein + membrane, then choose just the protein for
>> output.
>>
>> -Justin
>
>
> Hi Justin, thanks for replying so fast.
>
> So I have to create a group protein + membrane using index.ndx but I don't understand how to output the protein only.
> With the command gmx sasa, I just can choose the group of calculation and after that the program is already terminated, giving me a .xvg file and .pdb file.
> Can you explain me more steps please ?
>

Please provide the actual command you're using and all relevant output.

gmx sasa provides -surface and -output options.  These do what you want, 
provided you use a proper selection for each.

-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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