Re: [AMBER] pbsa eneopt = 4 option

From: Ray Luo <rluo.uci.edu>
Date: Wed, 12 Oct 2016 08:32:36 -0700

Hi Vlad,

Okay this is because the entry was not updated in the manual. Please
check the keyword combination in the test case for pb_np3m. The frcopt
should be 5 to match the eneopt=4. However, I think it should also
allow users to set frcopt=0, even if force is always computed.

All the best,
Ray

--
Ray Luo, Ph.D.
Professor
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Wed, Oct 12, 2016 at 7:44 AM, Vlad Cojocaru
<vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Dear Ray, Dear all,
>
> Using non linear Poisson Boltzmann, I thought of trying the option
> eneopt=4. However I always get the error: "PB Bomb in pb_read():
> combination of eneopt and frcopt is unsupported". I tried all possible
> values for frcopt option (0,1,2,3) and also I tried an input without
> defining frcopt at all (see below) but everytime the same error. Is the
> "eneopt=4" option usable whatsoever ?
>
> Thanks for answering
>
> Best wishes
> Vlad
>
>
>
> MMPBSA, Nonlinear PB, inp=2, sasopt=2
> &cntrl
>   nsnb=99999, dec_verbose=0, ioutfm=1,
>   ipb=2, ntb=0, cut=999.0, imin=5,
>   igb=10, inp=2,
> /
> &pb
>   epsin=4, epsout=80, smoothopt=1,
>   istrng=100.0, pbtemp=300, radiopt=1,
>   dprob=1.4, iprob=2.0, sasopt=2, saopt=0,
>   triopt=1, arcres=0.25,
>   npbopt=1, solvopt=1, accept=0.001,
>   maxitn=100, fillratio=4.0, space=0.5,
>   nbuffer=0, nfocus=2, fscale=8, npbgrid=1,
>   bcopt=5, eneopt=4, scalec=0,
>   cutfd=5.0, cutnb=15, nsnba=1,
>   phiout=0, npbverb=1,
>   decompopt=2, use_rmin=1, sprob=0.557, vprob=1.3,
>   rhow_effect=1.129, use_sav=1,
>   cavity_surften=0.0378, cavity_offset=-0.5692,
>   maxsph=400,
> /
>
> --
> Dr. Vlad Cojocaru
> Computational Structural Biology Laboratory
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
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Received on Wed Oct 12 2016 - 09:00:02 PDT