AMBER Archive (2008)

Subject: Re: AMBER: NONBONDED_PARM_INDEX

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 02 2008 - 10:04:26 CDT

On Wed, Jul 02, 2008, Max wrote:
>
>
> I would like to ask if anybody knows the meaning of the numbers
> in the NONBONDED_PARM_INDEX array, included in the prmtop file. I
> use Amber 8, and the information about this array, provided in
> http://amber.scripps.edu/formats.html seems to be not correct in my case. In
> fact, the formula index = ICO(NTYPES*(IAC(i)-1)+IAC(j)) cannot explain the
> values I find in my NONBONDED_PARM_INDEX array. More generally speaking, the
> only thing I don't understand of the prmtop file is how the various couples
> of atom types are assigned to the elements included in the 6-12 parameter
> arrays (or 10-12 parameter arrays).

The numbers don't depend on which version of Amber your have. To see how
the code really works, look for the variable "iaci" in egb.f. You may have to
run a small molecule and print out everything. I don't immediately see
that the documentation is incorrect (but it's early in the morning here).

...dac

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