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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Received on Thu Aug 18 2005 - 23:53:00 PDT
