AMBER Archive (2008)

Subject: Re: AMBER: topology file

From: David A. Case (case_at_scripps.edu)
Date: Wed Apr 16 2008 - 12:45:52 CDT

On Mon, Apr 14, 2008, Giuseppe De Marco wrote:
>
> I am trying to figure out how is defined the NONBONDED_PARM_INDEX
>
> According to the description in the topology format it should be a
> matrix (NTYPES*NTYPES), but is not very clear for me how the index
> values are calculated.
> By applying the formula : index = ICO(NTYPES*(IAC(i)-1)+IAC(j)) I don't
> get he same values shown in the NONBONDED_PARM_INDEX.

No, you shouldn't. The "index" you calculate above shows you where in the
CN1 and CN2 arrays to look for the Lennard-Jones parameters [i.e. you
look in CN1(index) and CN2(index).] See ew_directe.h for an example.

>
> In addition I would like to know if is possible to figure out the atoms
> involved in the Lennard Jones interactions considering the following
> parameters :
>
> -ATOM_TYPE_INDEX
> -NONBONDED_PARM_INDEX
> -LENNARD_JONES_ACOEF
> -LENNARD_JONES_BCOEF

See above.

...good luck...dac

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