Hi,
From the error, I guess you need to explicitly define the *strip_mask* on the command line.
Hope this helps.
Regards,
Zijian
________________________________
·¢¼þÈË: ZangRiran via AMBER <amber.ambermd.org>
·¢ËÍʱ¼ä: 2023Äê6ÔÂ27ÈÕ 15:20
ÊÕ¼þÈË: amber.ambermd.org <amber.ambermd.org>
Ö÷Ìâ: [AMBER] Keyerror about mmpbsa
Hello
I am running mmpbsa in amber18 using the following command" MMPBSA-1.py -O -i mmpbsa.in -o mmpbsa.dat -do final_mmpbsa.dat -sp com_solvated.prmtop -cp com.prmtop -rp ras.prmtop -lp raf.prmtop -y md.crd"
But I am encountering an error which says "Loading and checking parameter files for compatibility...
sander found! Using /mnt/disk1/software/AMBER18/amber18/bin/sander
cpptraj found! Using /mnt/disk1/software/AMBER18/amber18/bin/cpptraj
Preparing trajectories for simulation...
File "/mnt/disk1/software/AMBER18/amber18/bin/MMPBSA-1.py", line 99, in <module>
app.file_setup()
File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 156, in file_setup
self.mpi_size, str(external_progs['cpptraj']), self.pre)
File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line 104, in make_trajectories
traj.Strip(INPUT['ligand_mask'])
File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line 646, in Strip
raise InternalError('Cannot pass no mask to Strip!')
InternalError: Cannot pass no mask to Strip!
Exiting. All files have been retained."
How to rectify this kindly help as I am badly stuck in this.
Thank you,
Regards
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Received on Tue Jun 27 2023 - 20:30:02 PDT
