AMBER Archive (2005)

Subject: Re: AMBER: gaff frcmod file for TI calculation

From: Eric Hu (yhu_2003_at_yahoo.com)
Date: Wed Feb 02 2005 - 19:47:32 CST

Ok, I edited the frcmod file with all dummy atom
types. I only have a few things left. I use general
format for the dihedral parameters as follows:

DIHE
X -dc-dc-X 9 1.400 0.000 3.000
X -dc-dd-X 6 0.000 180.000 2.000
X -dc-do-X 3 1.150 0.000 3.000
X -dc-dn-X 9 1.400 0.000 3.000
X -dd-de-X 4 14.500 180.000 2.000
X -dd-do-X 2 5.400 180.000 2.000
X -de-de-X 4 14.500 180.000 2.000

However, leap still complains about some of the
torsions such as:

*** Proper torsion parameters missing ***
 atom names: C21-O20-C07-C06
 atom types: c-os-c3-c3 =pert=> dd-do-dc-dc
Please add a dummy parameter of multiplicity 1
for the pert types to your parameter set.
 - e.g. dd-do-dc-dc 1 0.0 0. 1.
(This is because multiple torsional potentials may
apply to a
single torsion, and each is perturbed individually in
gibbs.)

I already defined a general angel parameter X -do-dc-X
in the frcmod file. Why does this still happen? Also
it seems that leap hangs when using the regular form:

DIHE
dd-do-dc-dc 1 0.0 0. 1.
...

Eric

--- "David A. Case" <case_at_scripps.edu> wrote:

> On Wed, Feb 02, 2005, Eric Hu wrote:
>
> > Hi, I used antechamber to generate the frcmod file
> for
> > a small organic molecule. And it turns out the
> frcmod
> > file is empty. I then defined the dummy atom types
> in
> > the pert.frcmod file according to the atom types
> > generated by gaff. Now leap complains about all
> the
> > parameters (such as bond, angel and etc), which is
> > understandable. However is there a way to make the
> > pert.frcmod file without going to gaff.dat and
> > redefining all the missing parameters? Thanks.
>
> No, you have to do this by hand. There is no unique
> (or even "best") way
> to make dummy types, so it is hard to see how a
> program could really do this
> anyway.
>
> The perturbation stuff is quite flexible, but
> admittedly can be tedious to
> use.
>
> ...dac
>
>
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