This is a guess in the dark, but if an atom could somehow be bonded with
itself, perhaps this could result.
Bill
On 9/7/17 12:47 AM, 康宁 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.
>
> Thank you
> --------------------
> Regards,
>
> Kang Ning
> School of Pharmacy, Shanghai Jiaotong University
> M: 15821827306
> E: sherry.k_007.sjtu.edu.cn
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 07 2017 - 01:30:02 PDT
