AMBER Archive (2006)

Subject: Re: AMBER: LEaP Warning ... when do NH2-neutral fragment

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Jun 13 2006 - 16:23:18 CDT

> 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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