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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 26 2010 - 06:00:23 PDT
