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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 19 2013 - 10:30:03 PST
