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
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>
--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
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Received on Tue Nov 08 2011 - 22:30:03 PST
