AMBER Archive (2005)

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

From: Angela Liu (angela_ambermail_at_yahoo.com)
Date: Fri Aug 19 2005 - 12:44:03 CDT

Dear Anthony,

Thanks a lot! I missed that file while visiting the
formats website.
But that would mean that the NY line in the nonbon
section should not be there (parm99.dat) because the
NY is set to be equivalent to N, right? (Their R and
E are the same, so it didn't matter.)

Thank you again for taking your time to help!

Best wishes,
Angela

--- Anthony Fejes <fejes_at_zymeworks.com> wrote:

> 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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>
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