Hi,
In your print_res selection, it should be specified without a colon (:).
Check once.
*Satyajit Khatua*
On Fri, Jun 30, 2023 at 7:34 AM 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
> 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 141, in file_setup
> create_inputs(INPUT, self.normal_system, self.pre)
> File
> "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/createinput.py",
> line 56, in create_inputs
> com_card, rc_card, lc_card =
> prmtop_system.Group(INPUT['print_res'],True)
> File
> "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
> line 541, in Group
> rec_group_type, lig_group_type)
> File
> "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
> line 591, in _binding_group
> self._select_residues(selection)
> File
> "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
> line 829, in _select_residues
> raise SelectionError('Invalid selection! Integers expected.')
> SelectionError: Invalid selection! Integers expected."
> 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 Fri Jun 30 2023 - 00:00:02 PDT
