[gmx-users] about g_sas analysis

[Tsjerk Wassenaar]

Hi,

Recently there was a relatively extensive discussion on the list
regarding g_sas. Check the archives.

Cheers,

Tsjerk

On Thu, Mar 18, 2010 at 9:07 AM, Milan Melichercik
<melichercik at nh.usbe.cas.cz> wrote:
> supti mukherjee wrote:
>>
>> Dear gromacs users,
>> I have some doubts regarding the options to be selected in g_sas program.
>> g_sas asks for two groups, first one for calculation and second one for
>> output. As I have understood from the manual that first group should contain
>> all non solvent groups and second one the whole or part of these groups. Now
>> my doubt is that in a system of protein+ligand, when I am selecting both the
>> protein and ligand in option 1 ( in the calculation group) it automatically
>> is sending the second selected group to second option ( that is in the
>> output group). Is the solvent accessible area  given in terms of the output
>> group in the xvg file?
>>  I want to calculate solvent accessibility of the ligand which is
>> surrounded by the protein. Selecting what option can mimic that situation
>> most closely?
>> Regards
>> Supti
>> NIMHANS, BANGALORE
>>
>>
>>
> You need to create new group which contains atoms from both protein and
> ligand (make_ndx or by hand) and input number of this new group - the most
> of the programs reads only one group per input (the rest write something
> about selecting two groups...). Therefore the second number is read for the
> second input (as the group for output).
> About the rest of you question - I don't feel fully qualified to answer it
> and I hope, somebody will.
> Best.
>
> Milan
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands