[gmx-users] sas and index files

Marc Vogt mvogt at es.chem.umass.edu
Wed Nov 17 16:54:34 CET 2004

> > If i run g_sas with an index file representing some
> > portion of the molecule then does the program
> > calculate the area of thie portion defined by the
> > index file as a separate entity or in the context of
> > the whole protein?
> > 
> > If it takes the portion separately and calculates the
> > sas (without considering the rest of the protein) then
> > how do i calculate the area contributed by this porion
> > alone to the entire molecule?
> check the mailing list for recent changes. the  only correct version for
> computing partial areas is probably the CVS version
> > 

I think if you want the residue contribution to the SAS for a specific
pdb file or for an average over a time window for your trajectory
the 3.2.1 may work. 

If what you want is a plot of the residue SAS over time for the trajectory
you will need to compile the CVS code.  The input has changed from 3.2.1. 
The first part will ask you what you want to calculate it based on and you would
choose "Protein".  Then it asks again for an input and you can choose
which ever element you want from your index file, such as a residue.


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