Dear Sir,
We plan to calculate the electrostatic potential surface of a molecule using PBSA and also visualize the surface through PyMol. Following the Amber Tool User's Manual (p.143, v.11, sec.7.2.1) we used the following command:
pbsa -O -i mdin -o mdout -p prmtop -c inpcrd
However, the pbsa.phi file was not generated. We shall be thankful to know how the pbsa.phi file can be generated. the input (sec.7.3.2) used is given below:
&cntrl
ntx=1,
imin=1,
ipb=1,
inp=0
/
&pb
npbverb=1, istrng=0, epsout=80.0, epsin=1.0
space=1.0, accept=0.001
sprob=1.4, cutnb=9
phiout=1, phiform=0
/
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Received on Sun Mar 03 2013 - 22:00:02 PST
