[AMBER] A confusion about the binding energy calculated by pbsa with implicit membrane model

From: ÷ <zmgao1019.163.com>
Date: Wed, 12 Sep 2018 21:15:50 +0800 (CST)

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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 12 2018 - 06:30:04 PDT
Custom Search