> This is the warning in LEaP :
> > check as
> Checking 'as'....
> Warning: Close contact of 1.792161 angstroms between .R<ALD 1>.A<C 10> and
> .R<ALA 2>.A<N 1>
> Checking parameters for unit 'as'.
> Checking for bond parameters.
> Could not find bond parameter for: O - N
> Checking for angle parameters.
> Could not find angle parameter: O - N - H
> Could not find angle parameter: O - N - CT
> Could not find angle parameter: C - O - N
> There are missing parameters.
> check: Warnings: 1
> Unit is OK.
The first warning is nothing important. After minimization it will vanish.
But the rest of the messages mean that u need to defined the missing
parameters. For instance "Could not find bond parameter for: O - N" mean
that in the force field your are working on, there isnt any 'bond'
parameters defined for O -N. U have to prepare a modified force field file
(.frcmod file) and load it into Leap in order to create the necessary
prmtop/inpcrd files. Check out the example .frcmod files in
$AMBERHOME/dat/leap/parm directory. Good luck.
Best,
--
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 Wed Jun 14 2006 - 06:07:19 PDT
