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
>
>
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Received on Thu Dec 19 2013 - 10:00:03 PST
