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:
>
Make sure there is a title line (so &cntrl starts on the 2nd line). Also,
make sure you end the namelist with a "/" after the last namelist variable,
or "&end". I'm not sure if the first part is necessary, but it's always
worked for me (and I don't feel like checking the code to make sure :)).
HTH,
Jason
> &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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Oct 05 2011 - 08:00:06 PDT
