AMBER Archive (2009)

Subject: Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Sat Oct 31 2009 - 00:23:03 CDT

2009/10/30 Peter Schmidtke <pschmidtke_at_mmb.pcb.ub.es>:
> Thanks for the answer. Inherent question : The A & B coefficients are then
> given as a matrix of NTYPES x NTYPES, ntypes being the number of distinct
> atom types that exist in the system. They are sorted in increasing order in
> this matrix that is present in the prmtop file?

According to the documentation it's not NTYPES x NTYPES, it is
NTYPES*(NTYPES+1)/2), which you can verify by looking at a valid
prmtop file.

No particular ordering is imposed by CN1(ICO(NTYPES*(IAC(i)-1)+IAC(j)))...

--Tom

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