AMBER Archive (2005)

Subject: AMBER: parm99.dat non-bonded parameters

From: Angela Liu (angela_ambermail_at_yahoo.com)
Date: Thu Aug 18 2005 - 17:00:45 CDT


Dear Amber developers and users,

In the Amber parameter files such as parm99.dat
($AMBERHOME/dat/leap/parm/), not all atom types have
their non-bonded parameters defined. For instance,
only N, N3, and NY show defined R (radius) and E (well
depth) values among all the nitrogen atom types.
Other nitrogen types, NA, NB, NC, N2, N#, NT, and N*,
do not appear in the non-bonded section.

My questions are:
1) Is it LEaP that assigns the non-bonded parameters
for these atom types?
2) Is the assignment based on the hybridization states
and the element number?

Thanks a lot for your time and help!

Angela

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