Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between

From: case <>
Date: Mon, 26 Apr 2010 08:50:39 -0400

On Mon, Apr 26, 2010, Hyma vathi wrote:
> I am trying to simulate a protein with a cofactor, when I was trying to save
> the prmtop file the following message has come. Can anyone please tell how
> to sort out this problem. Thank you in advance.
> > saveamberparm comp comp_sol.prmtop comp_sol.inpcrd
> Checking Unit.
> WARNING: There is a bond of 8.894214 angstroms between:
> ------- .R<NAP 316>.A<O3B 18> and .R<NAP 316>.A<HO3 19>

The obvious questions: are these two atoms supposed to be bonded to each
other? Is there a bad distance in the input pdb file? If you use ambpdb to
convert comp_sol.inpcrd to a pdb-format file, and examine it visually, to
you get any clues to what has happened? Were the HO3 atom coordinates present
in the intial files? ..etc.

[Note: these are questions to help you debug the problem--you don't
necessarily have to provide answers to the list.]

...good luck...dac

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Received on Mon Apr 26 2010 - 06:00:23 PDT
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