AMBER Archive (2009)

Subject: Re: AW: [AMBER] Any Comment, please

From: s. Bill (
Date: Tue Aug 11 2009 - 03:22:16 CDT

Dear Susanne
Thanks so much for your interest.
I tested many protonation states of my inhibitor, using different techniques. But at the end of each day, I got wrong equilibrated structure.
May I ask you which method do you use, QM/MM or MM only? if MM only, do you use bonded or non-bonded model?
Thanks in advance

--- On Tue, 11/8/09, Aust, Susanne <> wrote:

From: Aust, Susanne <>
Subject: AW: [AMBER] Any Comment, please
To: "AMBER Mailing List" <>
Date: Tuesday, 11 August, 2009, 8:17 AM

Hello S. Bill,
I work also with an enzyme - ligand complex, where the ligand is coordinated
to a zinc atom. At my first dynamics the zinc atom goes during the
equilibration to a other amino acid for coordination, but this was in
disagreement to X-ray structure.
I solve the problem by thinking about the protonation state in the active
site. perhaps this hint can help you.
Good luck!

-----Ursprüngliche Nachricht-----
Von: []Im
Auftrag von s. Bill
Gesendet: 11 August 2009 09:56
Betreff: [AMBER] Any Comment, please


I am working on simulation of protein+ligand. According to the crystal
structural, the ligand bonds to Zinc active site of the protein by two
coordination bonds. I used QM/MM (PM3 Level) to simulate my system.
After minimization and heating (with constrain), the ligand lasted
bonded to the active site by two bonds. But, during equilibration, the
ligands started to change its position and formed ONLY one bond with the
zinc active site. I tried many models for the ligand and the active
site. but it didn't work.

I would appreciate any comment on what happened. Why the ligand didn't stay
bonded with two bonds as in the crystal structure?

Thanks in advance;

S. Bill

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