Dear Justin,<br><br>Firstly thanks for your valuable information. Now, <span id="result_box" class="short_text" lang="en"><span title="Alternatif çevirileri görmek için tıklayın" class="hps">is there</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">any error</span><span title="Alternatif çevirileri görmek için tıklayın" class="hps"></span></span>?<br>
Please see the following commands:<br><br>protein and ligand are merged by make_ndx<br><br>
g_sas -f run.xtc -s run.tpr -o area_protein.xvg -n protein_ligand.ndx<br>
Select a group for calculation of surface and a group for output<br>
<b>select a group: 1 (protein_ligand)</b><br>
<b>select a group: 2 (protein)</b><br>
<b>I have protein SASA.</b><br><br>g_sas -f run.xtc -s run.tpr -o area_ligand.xvg -n protein_ligand.ndx<br>
Select a group for calculation of surface and a group for output<br>
<b>select a group: 1 (protein_ligand)</b><br>
<b>select a group: 2 (ligand)<br>
I have ligand SASA.</b><br>
<br>
g_sas -f run.xtc -s run.tpr -o area_protein_ligand.xvg -n protein_ligand.ndx<br>
Select a group for calculation of surface and a group for output<br>
<b>select a group: 1 (protein_ligand)</b><br>
<b>select a group: 2 (protein_ligand)<br>
I have protein_ligand SASA.</b><br><br><b>(SASA between protein and ligand)=(protein)+(ligand)-(protein_ligand)</b><br><br>Thanks<br><br><div class="gmail_quote">2011/7/3 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear users,<br>
<br>
I want to compute SASA between protein and ligand.<br>
*1.)*<br>
protein and ligand are merged by make_ndx<br>
g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx<br>
Select a group for calculation of surface and a group for output<br>
select a group: 1 (protein+ligand)<br>
select a group: 2 (ligand)<br>
is this correct?<br>
<br>
*2.)*<br>
or<br>
g_sas -f run.xtc -s run.tpr -o protein_protein.xvg<br>
Select a group for calculation of surface and a group for output<br>
select a group: 1 (protein)<br>
select a group: 2 (protein)<br>
I have protein SASA.<br>
<br>
g_sas -f run.xtc -s run.tpr -o ligand_ligand.xvg<br>
Select a group for calculation of surface and a group for output<br>
select a group: 1 (ligand)<br>
select a group: 2 (ligand)<br>
I have ligand SASA.<br>
<br>
protein and ligand are merged by make_ndx<br>
g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx<br>
Select a group for calculation of surface and a group for output<br>
select a group: 1 (protein_ligand)<br>
select a group: 2 (protein_ligand)<br>
I have protein_ligand SASA.<br>
<br>
(SASA between protein and ligand)=(protein)+(ligand)-(<u></u>protein_ligand)<br>
<br>
I am confused. which of choices is correct?<br>
<br>
</blockquote>
<br></div></div>
Neither. Your equation is right, but your method of calculating each of the quantities is not. The group for the surface calculation should always be all non-solvent atoms (per the instructions in g_sas -h). The output group can then be whatever you like, a subset of that surface. So you will need three calculations (sort of like option #2), but in each case the calculation group should always be the protein-ligand merged group.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br><font color="#888888">
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</font></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>