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.
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
>
> _______________________________________________
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> AMBER.ambermd.org
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>
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Received on Wed Nov 09 2011 - 01:30:04 PST
