[gmx-users] Re: Re: calculation of standard deviation of SASA per residue

[Harpreet Basra]

 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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