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
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!"
And the input file MMPBSA content is "
&general
endframe = 10000,
verbose = 1,
strip_mask = ":WAT:CL:CLO:IB:K:LI:MG:NA:NB",
/
&gb
igb = 5, saltcon = 0.100,
/
&pb
istrng = 0.100,
/
&decomp
idecomp = 1, print_res = "1-77", dec_verbose = 1,
/"
How to rectify this kindly help as I am badly stuck in this.
Thank you,
Regards.
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Received on Sun Jul 02 2023 - 06:30:03 PDT
