Hello
Here are few old posts on this list with this kind of error and their
solutions
http://archive.ambermd.org/201104/0099.html
http://archive.ambermd.org/201412/0132.html >>> this will probably help to
resolve your issue.
Best Regards
On Mon, 9 Sep 2019 at 01:22, Johnny Guevara <johnnylguevara.gmail.com>
wrote:
> Hi,
>
> I have a protein-ligand system in which my ligand has an iodine atom type,
> and I keep getting this error message when running MMPBSA.py
>
> Beginning GB calculations with
> /global/common/cori/software/amber/14/hsw/bin/sander
> calculating complex contribution...
> bad atom type: i
> File "/global/common/cori/software/amber/14/hsw/bin/MMPBSA.py", line 104,
> in <module>
> app.run_mmpbsa()
> File
>
> "/global/common/cori/software/amber/14/hsw/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
>
> "/global/common/cori/software/amber/14/hsw/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
>
> "/global/common/cori/software/amber/14/hsw/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 157, in run
> self.prmtop))
> CalcError: /global/common/cori/software/amber/14/hsw/bin/sander failed with
> prmtop ache-ligand8.prmtop!
> Exiting. All files have been retained.
>
>
> Any ideas how to resolve this? I’ve tried different igbs and none work. Ive
> used mbondi2, using amber18. Ive attached my directory.
> MMGBSA.tar
> <
> https://drive.google.com/file/d/1SCto2D58bDW-hL_E9orNzr1s1aVh8Z5W/view?usp=drive_web
> >
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Received on Sun Sep 08 2019 - 23:00:01 PDT
