On Wed, Nov 9, 2011 at 4:17 AM, Xiao Chen <chen.xiao.po.gmail.com> wrote:
> Dear Dan,
>
> Thanks for the help, it solved my problem instantly!
> I am now able to calculate the SASA for each residue using cpptraj. As an
> output I get a file which contains SASA for 500 frames for each residues. I
> have 2 queries:
>
> a) Can I calculate the average of the SASA for each residue using cpptraj
>
b) Can I calculate the total Polar and Non-polar SASA for the entire
> protein both frame wise and average.
>
There is only solvent accessible surface area (SASA). There is no "polar"
SASA / "non-polar" SASA decomposition. There's a polar solvation term in
implicit solvent models (GB, PB, even RISM if you play tricks), and a
non-polar solvation term that is typically *related* to the SASA in crude
models (GB, PB -- RISM has a different way of doing it).
If you want to decompose both solvation terms for your protein, my
suggestion would be to use sander with the idecomp variable. MMPBSA.py
will automate this procedure for you if you do a so-called "stability
calculation". (Note you need Amber11 installed for MMPBSA.py to work).
These are detailed in the Amber manual (for sander) and AmberTools 1.5
manual (for MMPBSA.py).
Good luck,
Jason
> Thanks again!
>
> Regards,
>
> Po
>
>
> On Wed, Nov 9, 2011 at 11:53 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Hi,
> >
> > You can calculate the SASA for residues using the LCPO algorithm with
> > cpptraj:
> >
> > trajin mdcrd
> > surf res1sasa :1 out surf.dat
> > surf res2sasa :2 out surf.dat
> > ...
> >
> > where there is a 'surf' command for each residue you want calculated.
> > The output file 'surf.dat' will have the format
> >
> > #Frame res1sasa res2sasa ...
> >
> > -Dan
> >
> > On Wed, Nov 9, 2011 at 12:08 AM, Xiao Chen <chen.xiao.po.gmail.com>
> wrote:
> > > Hi All,
> > >
> > >
> > > I am trying to calculate the solvent accessible surface area of
> residues
> > > for an AMBER trajectory.
> > > I have looked into other posts regarding the same but I am unable to
> > > completely grasp on how can I do this
> > >
> > > I have the following input files:
> > > frames_dry.mdcrd (500 frames, waters have been stripped)
> > > frames_dry.prmtop
> > >
> > > and input file sasa.in
> > > &cntrl
> > > imin=5,
> > > gbsa=1,
> > > surften=1,
> > > &end
> > >
> > > can you please help me on how to
> > > a) modify this input file so as to I get SASA for each residue for the
> > > entire trajectory
> > > b) what exactly shall be the command I run to execute sasa.in
> > >
> > > Thanks much!
> > >
> > > Po
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Postdoctoral Associate
> > BioMaPS Institute, Rutgers University
> > 610 Taylor Road
> > Piscataway, NJ 08854
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Nov 09 2011 - 09:00:03 PST
