AMBER Archive (2005)

Subject: Re: AMBER: parm99.dat non-bonded parameters

From: Anthony Fejes (fejes_at_zymeworks.com)
Date: Fri Aug 19 2005 - 11:35:36 CDT

A good reference for questions like this is the Amber file format
specifications:

http://amber.scripps.edu/formats.html

In the section on Force field parameter file specifications, section 9
is "INPUT FOR EQUIVALENCING ATOM SYMBOLS FOR THE NON-BONDED 6-12
POTENTIAL PARAMETERS".

The corresponding lines in parm99.dat are:

N NA N2 N* NC NB NT NP NO NY
C* CA CB CC CD CK CM CN CQ CR CV CW CX CY CZ

These are used to set all of the Nitrogens that are not explicitly
mentioned otherwise in the 6-12 parameter section as equal to the type
N, and likewise, all of the C types that are not otherwise mentioned as C*.

I hope that helps,

Anthony Fejes

Angela Liu wrote:
> 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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