[gmx-users] Re: g_sas of ligands

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Sep 15 21:52:41 CEST 2011


The protein-buried hydrophobic area will only be considered if you use
a combined group comprising ligands and protein to calculate the
surface (and ligands only for output). If you use ligand only as group
for calculation and for output, you'll only get the area buried
between ligands.

Hope it helps,


On Fri, Sep 9, 2011 at 3:03 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Steven Neumann wrote:
>> Was my question not clear or noone can help me? I am wondering whether
>> calculations of ligand hydrophobic SAS (decrease during the simualtion) can
>> be result of binding to protein?
> Presumably it's due to both aggregation and binding to the protein, if, in
> fact both phenomena occur.  The extent of each effect will vary with time
> and you may have to analyze each ligand separately (i.e. do 30 calculations)
> to gather the detail you need.  In the absence of seeing the commands used
> to calculate the quantities you did, it's hard to comment further on any of
> the other points.
> -Justin
>>  On Fri, Sep 9, 2011 at 8:23 AM, Steven Neumann <s.neumann08 at gmail.com
>> <mailto:s.neumann08 at gmail.com>> wrote:
>>    Dear Gromacs Users,
>>         I am calculating SAS using g_sas of ligands in my system: protein,
>>    30 ligands in water. The hydrophobic SAS of ligands decrease and
>>    reach stable value. Hydrophilic remains stable over the simulation
>>    time. I am wondering whether it  (the decrease o hydrophobic) is
>>    because of binding to protein or aggregations of my small molecules
>>    (They do aggregate) or both? I mean: how is it caculated? Is binding
>>    to protein included in the decrease of the hydrophobic SAS of
>>    lignads or it is impossible and  aggregation will be the one thing?
>>         Thank you,
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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Tsjerk A. Wassenaar, Ph.D.

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

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