Date: Thu, 23 Jan 2003 12:07:14 +0100
From: Miguel de Federico
Subject: Re: Dummy-parameters in Amber?

I'm not an expert about this, but I think that really it doesn't matters
very much because you will define the name of the dummy atom that you want
in the frcmod.par. However, it seems coherent to name it "DC", because is a
Carbon which is perturbated to dummy.

Parameters are defined for dummy atoms as any other type of atom. Here you
have an exemple of parameters for perturbing "H" to nothing in
cyclohexanol, that I have used succesfully. You can make the changes you
need for your case.

--------------------------------------- dummyH.par
Parameters for dummy H in cyclohexanol.
MASS
DH 1.000 0.000

BOND
H1-DH 0.00 0.960

ANGLE
CT-H1-DH 0.000 109.400

DIHE
OH-CT-H1-DH 1 0.000 0. 3.
OH-CT-H1-DH 1 0.000 0. 1.
DH-H1-CT-CT 1 0.000 0. 3.
DH-H1-CT-CT 1 0.000 0. 1.
H1-CT-OH-HO 1 0.0 0. 3.
H1-CT-OH-HO 1 0.0 0. 1.
OH-CT-CT-H1 1 0.0 0. 3.
OH-CT-CT-H1 1 0.0 0. 1.
H1-CT-CT-H1 1 0.0 0. 3.
H1-CT-CT-H1 1 0.0 0. 1.


NONBON
DH 0.0000 0.0000

---------------------------------------

You should read the parameter file in LEaP when you want to create the
topology and coordinate files.

I hope this helps. It was quite difficult for me running my first FEP...

Miguel de Federico.

> Dear Ambers,
>
> I want to calculate a FEP for a organic molecule. My question is, when I
> perturb a "C" to nothing - what is the dummy? Is it DC or DH and how are
> the bonds, angles an torsions for the dummys defined?
>
> Thank you in advance,
>
> Heike