Dear Ray,
Thanks for information. I follow the Amber Tools manual. Take a small protein, create prmtop and inpcrd file, use the following command-
pbsa -O -i X.in -o X.out -p X.prmtop -c X.inpcrd
the X.in as below-
Sample PB visualization input
&cntrl
ntx=1,
imin=1,
ipb=1,
inp=0
/
&pb
npbverb=1, istrng=0, epsout=80.0, epsin=1.0,
space=1., accept=0.001,
sprob=1.4, cutnb=9,
phiout=1, phiform=0
/
It produce two file- X.out and pbsa.phi
But how can I see the potential surface in VMD is not given in the manual. Can I get a help? Please........
With best regards,
Sudarshan
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Received on Sat Apr 14 2012 - 06:30:04 PDT
