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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Received on Tue Jan 31 2017 - 08:00:02 PST
