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<div>Hi Mark,</div>
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<div>Thank you very much for your help. I got my answer. </div>
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<div>I chose protein as the group for calculating SASA and residue1 for output and i got the SASA of residue 1 vs time. This gave me the correct mean SASA of residue1 and also its std deviation. </div>
<div>I repeated the same way for all the residues and got SASA per residue with std deviation of each.</div>
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<div>Thanks again!!</div>
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<div>Regards,</div>
<div>Harpreet</div>
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<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">On 14/12/2011 4:01 PM, Harpreet Basra wrote:<br>> Hi<br>> I want to calculate the standard deviation of SASA of each residue of<br>
> a peptide. When using -or option for complete peptide in g_sas we get<br>> residue vs sasa only.<br><br>I don't follow what result you are describing as unsuitable for you needs.<br><br>> So i tried by creating an index file for each residue separately<br>
> (residue1.ndx, residue2.ndx and so forth) and then by calculating by<br>> using -o option i got time vs sasa for each residue, thinking that<br>> this will give me average sasa per residue as well as its standard<br>
> deviation. But I see that the average value obtained by this method<br>> for each residue is different from the one i got by using -or option<br>> (and calculating for complete peptide). Why is it so? Doesnt -or<br>
> option gives average sasa over entire trajectory per residue? Can<br>> anyone suggest any way to compute the standard deviation?<br>><br><br>It's hard to comment when we don't know which groups you chose for which<br>
calculation. Using an index file to change *only* the output group and<br>using g_sas -or should definitely work, but I don't see why custom<br>groups should be needed at all.<br><br>Mark<br><br></blockquote></div>