AMBER Archive (2008)
Subject: AMBER: NONBONDED_PARM_INDEX
From: Max (reshouldered_at_hotmail.com)
Dear Amber community,
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).
Thank you very much