Hi,
Can you please check the compatibility of the four prmtop files? As far as
I know, the default setting for the strip_mask is enough to do the
subsequent calculation of binding free energy. From the following lines
" 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!')",
there may be some problem in selecting ligand msk (I guess). Are you trying
to reproduce the data given in the MMPBSA.py tutorial (
https://ambermd.org/tutorials/advanced/tutorial3/py_script/section6.php)?
*Best,*
*Satyajit Khatua*
On Tue, Jun 27, 2023 at 12:50 PM ZangRiran via AMBER <amber.ambermd.org>
wrote:
> 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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>
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Received on Wed Jun 28 2023 - 02:00:02 PDT
