The program is saying that the calculation failed with sander. So check the
mdout files generated by MMPBSA.py. The actual error message should be near
the bottom of one of those mdout files.
-Bill
On Tue, Jul 11, 2023 at 10:20 PM Riran via AMBER <amber.ambermd.org> wrote:
> The pdb indicates that it is MN, but I remove MN from display" File
> "/mnt/disk1/software/AMBER18/amber18/bin/MMPBSA-1.py", line 100, in
> <module><br/> app.run_mmpbsa()<br/> File
> "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa<br/> self.calc_list.run(rank, self.stdout)<br/>
> File
> "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run<br/> calc.run(rank, stdout=stdout, stderr=stderr)<br/>
> File
> "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 157, in run<br/> self.prmtop))<br/>CalcError:
> /mnt/disk1/software/AMBER18/amber18/bin/sander failed with prmtop
> com-3.prmtop!<br/>Exiting. All files have been retained."<br/>I don't know
> how to solve this problem. Can you help me?<br/>Thanks
> From: David A Case via AMBER <amber.ambermd.org>
> Date: 2023-07-07 23:57:59
> To: Riran <2115391084.st.gxu.edu.cn>,AMBER Mailing List <
> amber.ambermd.org>
> Subject: Re: [AMBER] Error while running mmpbsa>On Fri, Jul 07, 2023,
> Riran via AMBER wrote:
> >
> >>I tried what you suggested, but it didn't work out. I tried MN , Mn2+,
> Mn,
> >>but none of them worked.
> >
> >Use (for example) ambpdb to create a pdb file for your system, and see
> what
> >the residue names are in your particular system. The PDB (and Amber)
> >standard is to use MN as the residue name for manganese.
> >
> >Aside: you use of Na+ and Cl- is also non-standard: the correct names are
> NA
> >and CL. I'm not sure you you prepared the system to get these names.
> (This
> >is a curse of backwards-compatibilty: in the previous millenium, after the
> >deluge but before the internet, Amber developers started using Na+ and
> Cl-.
> >We somewhat foolishly tried to keep this as an alternative (for just these
> >two ions plus K+), but that inevitably leads to confusion.)
> >
> >....dac
> >
> >
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> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
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>
--
Bill Miller III
Assistant Professor of Chemistry
Truman State University
417-549-0952
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Received on Wed Jul 12 2023 - 08:00:03 PDT
