> On Feb 2, 2015, at 2:22 AM, chemjxn.126.com wrote:
>
> Hello, all
> I want to parameterization Zn2+ in the protein - ligand complex. Could I divided the Zn2+ into ligand? And what can I do, in the next. I'm a junior. Please help me! Thank you very much!
There are two main approaches you can take here. The first is to model the zinc atom as a single ion that is not covalently bound to anything (but instead binds interacts via non-covalent interactions). In this case, the ion parameters for Zn2+ have already been defined in one of the divalent metal ion parameter files for a handful of water models. See chapter 3 (I believe section 8) for more information about ion parameters (Amber 14 manual).
If your system requires the Zn2+ to be covalently bound to some part of the system, the task becomes much more difficult. The MCPB program was written to help parametrize metal ion centers (stands for Metal Center Parameter Builder), and will help build both a library file (with charges and connectivity) as well as parameters for the molecule you can load in tleap. See the MCPB tutorial (
http://ambermd.org/tutorials/advanced/tutorial20/ <
http://ambermd.org/tutorials/advanced/tutorial20/>) for a walkthrough on how to use that program.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Feb 02 2015 - 05:30:04 PST
