Hi,
Can you open one of the *mdout files generated and see what error is being
printed?
Thanks,
Dwight
On Tue, Jan 31, 2017 at 10:41 AM, Albert <mailmd2011.gmail.com> wrote:
> I add this option in the mmpbsa.in as following:
>
> &general
> endframe=100, verbose=1, use_sander=1
> /
> &gb
> igb=2, saltcon=0.150
> /
> &pb
> istrng=0.150, fillratio=4.0
> /
>
>
> unfortunately it failed with similar errors:
>
> > MMPBSA.py -O -i 06-mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> sol.prmtop -cp com.prmtop -rp rec.prmtop -lp lig.prmtop -y prod*.mdcrd
>
> Loading and checking parameter files for compatibility...
> sander found! Using /home/albert/install/amber16/bin/sander
> cpptraj found! Using /home/albert/install/amber16/bin/cpptraj
>
> Preparing trajectories for simulation...
> 100 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with /home/albert/install/amber16/bin/sander
> calculating complex contribution...
> File "/home/albert/install/amber16/bin/MMPBSA.py", line 100, in
> <module>
> app.run_mmpbsa()
> File
> "/home/albert/install/amber16/lib/python2.7/site-packages/
> MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/home/albert/install/amber16/lib/python2.7/site-packages/
> MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/home/albert/install/amber16/lib/python2.7/site-packages/
> MMPBSA_mods/calculation.py",
> line 157, in run
> self.prmtop))
> CalcError: /home/albert/install/amber16/bin/sander failed with prmtop
> com.prmtop!
> Exiting. All files have been retained.
>
>
>
> On 01/31/2017 04:07 PM, Vlad Cojocaru wrote:
> > Please look in the manual at how to run MMBPSA ... There is a keyword
> > that allows you to instruct the script to use sander ....
> >
> >
>
>
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>
--
T. Dwight McGee Jr.
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Tue Jan 31 2017 - 09:00:02 PST
