AMBER Archive (2009)

Subject: Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Fri Oct 30 2009 - 17:04:43 CDT

> First question : what is CN1, I suppose a program internal variable?

Yes, cn1, cn2, et cetera are variables in the source code. Even if you
don't know Fortran, you can look at rdparm.f for clues about what
variable name corresponds to what block type - e.g.
LENNARD_JONES_ACOEF, BOND_FORCE_CONSTANT are (relatively) easy to
figure out. Some of the other ones, however, are a bit more opaque.

> The number of atom types are respective to the forcefield or only
> respective to the current structure?

They are with respect to that particular prmtop file.

> Where can I find all the input files for reading the atom type indices,
> CN1, CN2, ASOL, BSOL for the amber 99 ff?

These are assembled from the force field files in
$AMBERHOME/dat/leap/. See, for example, leaprc.ff99 to see exactly
which files it reads. Once the prmtop and inpcrd are created you don't
need any other files to get all the parameters you need for that
particular simulation.

--Tom

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