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.
Hope this is helpful.
-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!
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 10 2011 - 13:00:04 PDT
