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 Sun Oct 09 2011 - 17:00:03 PDT
