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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