Is there any method to calculate binding free energy of a metal ion to a protein?
Thanks.
--------------------
Regards,
Kang Ning
E: sherry.k_007.sjtu.edu.cn
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Date: Thu, 7 Sep 2017 01:11:27 -0700
From: Bill Ross <ross.cgl.ucsf.edu>
Subject: Re: [AMBER] Error in MM-PBSA -- BondError: Cannot exclude an
atom from itself
To: amber.ambermd.org
Message-ID: <0200232d-eb53-d056-c93d-9b607a082fbe.cgl.ucsf.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
This is a guess in the dark, but if an atom could somehow be bonded with
itself, perhaps this could result.
Bill
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 Fri Sep 08 2017 - 18:30:04 PDT
