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
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Received on Thu Sep 07 2017 - 01:00:02 PDT
