AMBER Archive (2003)

Subject: AMBER: torsion problems of dummy atoms

From: Difei Wang (dwang_at_nd.edu)
Date: Mon Nov 24 2003 - 14:24:11 CST

Dear All,

I am perturbating a CH3CO2- to nothing, ie,

       h1 o dh do
        | | | |
h1---c3----c----o -------> dh----dz----dc-----do
        | |
       h1 dh
 
When I tried to save the pert and crd files. I gave me this message,

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> saveamberparmpert aco1 aco.FEP.ptop aco.FEP.crd
Checking Unit.
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
.........
*** Improper torsion parameters missing ***
 atom names: O2-O4-C13-C12
 atom types: o-o-c-c3 =pert=> do-do-dc-dz
Please add a dummy parameter of multiplicity 2
for the pert types to your parameter set.
 - e.g. do-do-dc-dz 0.0 0. 2.
(This is because multiple torsional potentials may apply to a
single torsion, and each is perturbed individually in gibbs.)
 total 1 improper torsion applied
Building H-Bond parameters.
Parameter file was not saved.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

It seems the improper torsion parameter is missing. So how to input it
in the dummy parameter file? I tried to add " do-do-dc-dz 0.0 0. 2."
in the DIHE section. But it asked me again. Here is my parameter file.

~~~~~~~~~~~
meco2- to nothing with bond shrinkage
MASS
dh 1.008 dh IS DUMMY HYDROGEN
dc 12.01 dc dummy carbon in C=O
do 16.00 do dummy oxygen in C=O
dz 12.01 dz dummy carbon

BOND
do-dc 340.0 0.2 Note that "dummy" bond does shrink
dz-dh 340.0 0.2
dc-dz 340.0 0.2

ANGLE
do-dc-do 80.0 120.0
do-dc-dz 70.0 120.0
dc-dz-dh 50.0 109.5
dh-dz-dh 35.0 109.5

DIHE
do-dc-dz-dh 1 0.0 0. 1.
do-dc-dz-dh 1 0.0 0. 3.
do-do-dc-dz 0.0 0. 2.

NONB
dh 0.000 0.0000
do 0.000 0.0000
dc 0.000 0.0000
dz 0.000 0.0000
~~~~~~~~

Any comments will be appreciated.

Difei
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Difei Wang, Ph.D.
Department of Chemistry and Biochemistry
University of Notre Dame
Notre Dame, IN
USA

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