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 - 03:00:02 PST
