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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Received on Tue May 17 2005 - 01:53:00 PDT
