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