Thank you for reply Sir. These two atoms are not supposed to have any bond
between them. Initially there were two HO3 atoms present in original pdb,
whereas after converting the prmtop to pdb there is only one HO3 atom and
the other has changed to O3. I have no clues what to do.
On Mon, Apr 26, 2010 at 9:50 PM, case <case.biomaps.rutgers.edu> wrote:
> 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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>
--
Hymavathi,
MS(Pharm),
Center for Pharmacoinformatics,
National Institute of Pharmaceutical Education and Research(NIPER),
Mohali,
INDIA.
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Received on Mon Apr 26 2010 - 10:00:06 PDT
