# Re: [AMBER] How to Calculate SASA with Amber?

From: Oliver Grant <olivercgrant.gmail.com>
Date: Tue, 11 Oct 2011 10:13:10 +0100

Hi all,

For the picture you can also take your calculated residue or even atom SASA
values and put them into the b-factor column of your pdb. You can then
colour by b-factor in VMD.

Oliver

On 10 October 2011 20:55, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> Hi,
>
> I'm not sure I completely understand what you're asking, but you can
> specify a mask with the 'surf' command in cpptraj; this will calculate
> the contribution to the overall SASA by the atoms in the mask. So, for
> example given this cpptraj input:
>
> parm protein.parm7
> trajin trajectory.nc
> surf R1 :1 out sasa.dat
> surf R2 :2 out sasa.dat
> surf R3 :3 out sasa.dat
>
> You will get an output file (sasa.dat) that will contain the SASA of
> residues 1, 2, and 3, like so:
>
> #Frame R1 R2 R3
>
> Note that here R1, R2, and R3 are just labels, you can name it
> whatever you want.
>
>
> -Dan
>
> On Sun, Oct 9, 2011 at 7:53 PM, qiao xue <xueqiaoup.gmail.com> wrote:
> > Thank you very much. I have used this LCPO method and it works.
> >
> > May I ask another question? This LCPO method could calculate the SASA
> > of trajectory. I see some paper also has some SASA pic that it is the
> > SASA of every residue. How to make this kind of picture? Does it need
> > to get a average structure of mdcrd and then Calculate the SASA? Or
> > Amber has some other method?
> > Thanks
> >
> > 2011/10/6, Daniel Roe <daniel.r.roe.gmail.com>:
> >> Hi,
> >>
> >> You can also calculate SASA via the LCPO method using cpptraj,
> >> available with AmberTools 1.5.
> >>
> >> -Dan
> >>
> >> On Wed, Oct 5, 2011 at 6:53 AM, qiao xue <xueqiaoup.gmail.com> wrote:
> >>> Hello all,
> >>>
> >>> I am trying to calculate the "solvent accessible surface area"(SASA)
> >>> of a molecule through a trajectory file obtained by AMBER10. I use the
> >>> GB model.
> >>>
> >>> I searched some scripts and used it directly. But it shows "could not
> >>> find cntrl namelist" in sasa.out. And the script I used is this:
> >>>
> >>> &cntrl
> >>> imin=5, igb=5, gbsa=2,
> >>> ntx=1, maxcyc=0,
> >>> ntc=1, ntf=1,
> >>> ntb=0, ntp=0,
> >>> surften=1,
> >>> ntwe=0, ntpr=500, ntwx=1,
> >>> cut=1000,
> >>>
> >>> \$AMBERHOME/exe/sander -O -i sasa.in -p prmtop -x mdcrd -c rst -o
> sasa.out
> >>> I don't know why. It seems that the calculation of SASA is different
> >>> with other analytical tools. I really wish Someone would help me.
> >>>
> >>> Thanks!
> >>>
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> >>>
> >>
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Received on Tue Oct 11 2011 - 02:30:02 PDT
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