Hi,
I don't know if this is a writting mistake or not. You command line reads
" MMPBSA-1.py<
http://mmpbsa-1.py/> -O -i mmpbsa.in<
http://mmpbsa.in/> -o mmpbsa.dat -do final_mmpbsa.dat -sp com_solvated.prmtop -cp com.prmtop -rp ras.prmtop -sp raf.prmtop -y md.crd"
But for ligand prmtop, it should be -lp keyword, not the -sp.
Best,
Satyajit Khatua
________________________________
From: Ray Luo via AMBER <amber.ambermd.org>
Sent: Monday, June 26, 2023 8:30:59 PM
To: 余鸿艳 <1915391047.st.gxu.edu.cn>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Keyerror about mmpbsa
How about just upgrading to AmberTools 23 instead? It's free.
All the best,
Ray
--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Sun, Jun 25, 2023 at 10:17 PM 余鸿艳 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 -sp raf.prmtop -y md.crd"
> But I am encountering an error which says "
> Loading and checking parameter files for compatibility...
> File "/mnt/disk1/software/AMBER18/amber18/bin/MMPBSA-1.py", line 98, in <module> app.loadcheck_prmtops()
> File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 574, in loadcheck_prmtops
> FILES.receptor_prmtop, FILES.ligand_prmtop)
> File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py", line 102, in __init__ self.ligand_prmtop = LoadParm(ligand_prmtop)
> File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/ParmEd-3.0.0+57.g74a84d30-py2.7-linux-x86_64.egg/parmed/amber/readparm.py", line 70, in LoadParm parm = parm.view_as(AmberParm)
> File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/ParmEd-3.0.0+57.g74a84d30-py2.7-linux-x86_64.egg/parmed/amber/amberformat.py", line 426, in view_as return cls.from_rawdata(self)
> File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/ParmEd-3.0.0+57.g74a84d30-py2.7-linux-x86_64.egg/parmed/amber/_amberparm.py", line 266, in from_rawdata inst.initialize_topology()
> File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/ParmEd-3.0.0+57.g74a84d30-py2.7-linux-x86_64.egg/parmed/amber/_amberparm.py", line 207, in initialize_topology self.load_pointers()
> File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/ParmEd-3.0.0+57.g74a84d30-py2.7-linux-x86_64.egg/parmed/amber/_amberparm.py", line 450, in load_pointers
> self.pointers["NATOM"] = self.parm_data["POINTERS"][NATOM]
> KeyError: 'POINTERS'
> 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 Mon Jun 26 2023 - 09:00:02 PDT
