I believe sasopt will be forcibly set to 0 whenever inp=1, even if sasopt
is explicitly set to 1 in the input file. This is built into the pbsa
option reading routine.
Looking through the code, it seems that if you were to set sasopt=1 and
inp=1 it will simply print out a warning message telling you that it is
reseting the sasopt to 0.
-Wes
> 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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>>
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Received on Thu Dec 19 2013 - 12:00:03 PST
