On Tue, Nov 08, 2011, 刘吉元 wrote:
>
> I need to simulate a protein with two manganese ions,I have import the
> MN2+ parameters that download from
> www.pharmacy.manchester.ac.uk/bryce/amber.Because in my situation the Mn2+
> is coordinated both to amino acid both to ligand,so I bond these atoms each
> other.
If you do that, you have to tell Amber what parameters to use for the new
bonds you have made.
> Could not find bond parameter for: O2 - MN
> Could not find bond parameter for: NA - MN
These sorts of messages mean that Amber doesn't know how to treat these bonds.
You will need to create a frcmod file that has that information. That is not
a trivial task, unless you are following a literature procedure where such
information might be available. There is no automated or general way in Amber
to handle transition metal ions.
....dac
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Received on Thu Nov 10 2011 - 06:30:04 PST
