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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Received on Wed Oct 05 2011 - 04:00:02 PDT
