On Thu, Sep 7, 2017 at 3:47 AM, 康宁 <sherry.k_007.sjtu.edu.cn> wrote:
> Hi all,
> I want to calculate the binding free energy of a metal ion to protein, and
> I set the metal ion as ligand,
> But when I used MM-PBSA to calculate via amber14, an error occurred:
>
> “BondError: Cannot exclude an atom from itself”
>
> If I added an water molecule to the ligand, mmpbsa could work. So the top
> file, crd file and input file is correct. But I still want the result just
> containing metal ion and protein.
>
> If anybody could suggest something that would be helpful.
>
It looks like there is something wrong with one of your topology files.
In particular, the exclusion list for one of the atoms seems to include
itself. I've checked that ParmEd works for single-atom topology files and
it does, so I'm not sure what's happening here.
Can you attach your prmtop file so we can reproduce the issue?
Thanks,
Jason
--
Jason M. Swails
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Received on Sat Sep 09 2017 - 19:30:02 PDT
