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

From: Ray Luo <rluo.uci.edu>
Date: Wed, 12 Sep 2018 10:35:32 -0700

Hi Zhenmei,

EPB is included as part of EELEC in the membrane calculations in pbsa,
which is the total electrostatics energy. If you want to know how much
is EPB, you can first do a gas phase calculation to obtain the Coulomb
energy, so the difference of the EELEC and the Coulomb would be EPB.

This behavior is different from that in globular proteins because a
different energy output option has to be used.

VDWAALS is for the total pairwise vdw energy of all solute atoms.

All the best,
Ray 
--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical Physics, Biomedical Engineering, and Chemical Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Wed, Sep 12, 2018 at 6:15 AM, 高振梅 <zmgao1019.163.com> wrote:
> 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 - 11:00:03 PDT
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