Dear AMBER,
Recently, I'm learning how to calculate the binding energy of membrane protein by pbsa (in ambertools17) with implicit membrane model.
There is a test in the $AMBERHOME/AmberTools/test/pbsa_memb_test,
the command in "Run.memb.test" is:
&cntrl
ntx=1, imin=1, ipb=1, inp=0
/
&pb
npbverb=0, epsout=80, epsin=1, epsmemb=4, radiopt=0,
dprob=1.4, sasopt=0, membraneopt=1, mthick=20.0,
space=1.0, fillratio=2, nfocus=1, solvopt=1
accept=1e-4, maxitn=1000, mprob=2.29,
bcopt=10, eneopt=1, cutnb=99.0, cutfd=7.0,
/
while the final result in "aquaporin_coil.out.save" is:
NSTEP = 1 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -1625.1537 EKtot = 0.0000 EPtot = 0.0000
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 64.8739
EELEC = -1690.0276 EPB = 0.0000 RESTRAINT = 0.0000
ECAVITY= 0.0000 EDISPER = 0.0000
I can't understand why EPB is zero, and what does EELEC and VDWAALS correspond to?
Thank you in advance.
Zhenmei Gao
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Received on Wed Sep 12 2018 - 06:30:04 PDT
