AMBER Archive (2004)

Subject: Re: AMBER: Adding residues

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• Maybe in reply to: yen li: "AMBER: Adding residues"
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>> Could you please tell me what file (files) contain the
>> atomic charges, R* and epsilon values for metal ions like
>> Fe, Mg ...etc in amber?
>
> Look in your AMBERHOME/dat/leap/parm/ directory.
> I believe the values you
> are looking for will be in a parm*.dat file (i.e. parm99.dat)

The atomic charges depend on the bond context of each atom,
so are in the prep.in or leap.lib files. For ions there is
AMBERHOME/dat/leap/lib/ions91.lib and AMBERHOME/dat/leap/ions94.lib -
see the ions*.cmd scripts to see how the libs are built.

Bill
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• Next message: Sebastian Fernandez Alberti: "AMBER: resp charge calculation for Fe+3 heme"
• Previous message: jz7_at_duke.edu: "AMBER: question about covariance matrix from ptraj"
• Maybe in reply to: yen li: "AMBER: Adding residues"
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