Vlad,
Okat, input file looks fine to me. Can you email me off the list a few
snapshots for us to reproduce your error?
Ray
On Dec 19, 2013 10:30 AM, "Vlad Cojocaru" <vlad.cojocaru.mpi-muenster.mpg.de>
wrote:
> Hi Ray,
>
> Below is the input and the running command (using the _MMPBSA_pb.mdin
> file from my previous email)...
>
> Best wishes
> Vlad
>
>
>
> cat << EOF > mmpbsa.in
> MMPBSA
> &general
> debug_printlevel=0,
> startframe=1,
> endframe=50000,
> interval=1,
> keep_files=1,
> netcdf=1,
> ligand_mask=":1-152",
> receptor_mask=":153-283",
> use_sander=1,
> entropy=0,
> full_traj=1,
> verbose=2,
> /
> &pb
> inp=1,
> cavity_offset=0.86,
> cavity_surften=0.005,
> indi=1.0,
> exdi=80.0,
> fillratio=4.0,
> istrng=0.100,
> linit=1000,
> prbrad=1.4,
> radiopt=0,
> scale=2.0,
> /
> EOF
>
> $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in \
> -o mmpbsa.out \
> -cp complex.top \
> -rp receptor.top \
> -lp ligand.top \
> -y complex.cdf \
> -eo energy.out \
> -use-mdins
>
>
>
>
> On 12/19/2013 06:40 PM, Ray Luo, Ph.D. wrote:
> > Vlad,
> >
> > Please show us your "mmpbsa.in" file.
> >
> > Ray
> > On Dec 19, 2013 2:40 AM, "Vlad Cojocaru" <
> vlad.cojocaru.mpi-muenster.mpg.de>
> > wrote:
> >
> >> Dear all,
> >>
> >> I am trying an MMPBSA calculation (AmberTools 13) with inp=1 (see input
> >> file below). However I get a PB Bomb error (see below).
> >> Now, reading through the list archive, it was reported a while ago
> >> (2011) that this might have something to do with sasopt=1 in the input
> >> file. Howeever, this is required for inp=1 ... That thread had no
> >> answers though. Does anybody have any experience with this type of
> >> errors ? Anything obviously wrong in my input ?. I created the input
> >> upon systematically reading the original literature on the parameters .
> >>
> >> Thanks for any advice on this,
> >>
> >> Best wishes
> >> Vlad
> >>
> >>
> >> ****************** Sander input for PB calculation *********************
> >> File generated by MMPBSA.py
> >> &cntrl
> >> nsnb=99999, dec_verbose=0, ioutfm=1,
> >> ipb=2, ntb=0, cut=999.0, imin=5,
> >> igb=10, inp=1,
> >> /
> >> &pb
> >> epsin=1, epsout=80, smoothopt=1,
> >> istrng=100.0, pbtemp=300, radiopt=0,
> >> dprob=1.4, iprob=2.0, sasopt=1, saopt=0,
> >> triopt=1, arcres=0.25,
> >> npbopt=0, solvopt=1, accept=0.001,
> >> maxitn=100, fillratio=4.0, space=0.5,
> >> nbuffer=0, nfocus=2, fscale=8, npbgrid=1,
> >> bcopt=5, eneopt=2, frcopt=0, scalec=0,
> >> cutfd=5.0, cutnb=0, nsnba=1,
> >> phiout=0,
> >> decompopt=2, use_rmin=1, sprob=1.4, vprob=1.4,
> >> rhow_effect=1.0, use_sav=0,
> >> cavity_surften=0.005, cavity_offset=0.86,
> >> maxsph=400,
> >> /
> >>
> >> ****************** Error *****************************
> >> PB Bomb in assignlvlset(): no atmsas 105 97 7
> >> 103 95 9 -2
> >> 103 95 9 -2
> >> 103 95 9 -2
> >> 103 95 9 -2
> >> 103 95 9 -2
> >> 103 95 9 2
> >> 103 95 9 -2
> >> PB Bomb in assignlvlset(): illegal insas flag 105 97 7 -4
> >>
> >> --
> >> Dr. Vlad Cojocaru
> >> Max Planck Institute for Molecular Biomedicine
> >> Department of Cell and Developmental Biology
> >> 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/research/teams/groups/rgcojocaru
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
> --
> Dr. Vlad Cojocaru
> Max Planck Institute for Molecular Biomedicine
> Department of Cell and Developmental Biology
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>
>
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Received on Thu Dec 19 2013 - 11:00:02 PST
