AMBER Archive (2005)

Subject: AMBER: *** Proper torsion parameters missing ***

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon May 16 2005 - 19:19:04 CDT


Dear AMBER list,

I am trying to create a perturbation prmtop and inpcrd file for a
structure. I am getting the following error(s):
---------------------------------------------------
Building proper torsion parameters.
*** Proper torsion parameters missing ***
 atom names: C6-C5-C4-N4
 atom types: CM-CM-CA-N2 =pert=> CM-CM-C-O
Please add a dummy parameter of multiplicity 3
for the non-pert types to your parameter set.
 - e.g. CM-CM-CA-N2 1 0.0 0. 3.
(This is because multiple torsional potentials may apply to a
single torsion, and each is perturbed individually in gibbs.)
---------------------------------------------------
The parameter used for CM-CM-CA-N2 is

X -CA-CM-X 4 10.20 180.0 2. intrpol.bsd.on
C6H6

The parameter used for CM-CM-C -O is

CM-CM-C -O 1 2.175 180.0 -2. Junmei et al,
1999
CM-CM-C -O 1 0.30 0.0 3. Junmei et al,
1999

Xleap is saying that I should add a dummy parameter for CM-CM-CA-N2
such that its gonna yield a 'zero' energy. The suggested parameter

CM-CM-CA-N2 1 0.0 0. 3

will yield a 'zero' energy. But why do we need to add this info? It is
already defined above by

X -CA-CM-X 4 10.20 180.0 2.

And also I do not understand the error message, saying "This is because
multiple torsional potentials may apply to a single torsion, and each is
perturbed individually in gibbs.". I am not gonna use gibbs. I will
appreciate if someone can tell me what this error message means. Thanks in
advance.

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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