Re: [AMBER] pbsa:cannot match namelist object name mprob

From: Ray Luo <rluo.uci.edu>
Date: Mon, 17 Sep 2018 10:15:21 -0700

Zhenmei,

Yes indeed mprob = 2.7 by default so you don't have to specify it in
the input file.

In mmpbsa.py, it's not offered as a changeable keyword, which is why
you saw that error message.

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 Mon, Sep 17, 2018 at 7:00 AM, 高振梅 <zmgao1019.163.com> wrote:
> Dear AMBER,
>
>
> Recently, I'm calculating the binding energy of membrane protein by pbsa (amber16) with implicit membrane model.
>
>
>
> There I am getting the following the message:
> "Cannot match namelist object name mprob
> namelist read: misplaced = sign
> Cannot match namelist object name .7"
>
>
> The code in the  file that pbsa is trying to read 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=32.0,
>    space=0.5, fillratio=2, nfocus=1, solvopt=1,
>    accept=1e-4, maxitn=1000, mprob=2.70,
>    bcopt=10, eneopt=1, cutnb=10, cutfd=7.0,
>  /
> When I remove this parameter(mprob=2.70), there is no such information. But the two result calculated is the same.
>
> the final result in out.file is:
> NSTEP =        1   TIME(PS) =       0.000  TEMP(K) =     0.00  PRESS =     0.0
>  Etot   =    -82722.3621  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    =     -7368.7223
>  EELEC  =    -75353.6398  EPB     =         0.0000  RESTRAINT  =         0.0000
>  ECAVITY=         0.0000  EDISPER =         0.0000
>
> According to the manual, the MPROB is Membrane probe radius (default 2.70 Å), which is used to specify the highly different lipid molecule accessibility versus that of the water. So I wonder if I can ignore this message because of the same results. If not, what should I do?
>
> Thank you in advance.
> Zhenmei Gao
>
>
>
>
>
>
>
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Received on Mon Sep 17 2018 - 10:30:02 PDT