Dear David,
Yes, it was an error in specifying residue connectivity in the tleap script.
I kept ligands at the end of pdb but forgot to make adjustments in bond
command.
After fixing that all seems to be correct as shown by parmed >>
checkvalidity
thanks for your suggestions.
On Mon, May 3, 2021 at 5:56 PM David A Case <david.case.rutgers.edu> wrote:
> On Mon, May 03, 2021, Vaibhav Dixit wrote:
>
> >Error: Atom 9656 was assigned a lower molecule # (1) than previous atom
> (2).
>
> Look at atom 9695 and its previous atom. Is the former part of molecule 1
> and that latter a part of molecule 2? Can you see a simple way to fix
> this?
> Sometimes, reordering ligand or solvent molecules can obviate such a
> problem.
>
> Also it's not clear whether you tried the fixes that are mentioned in the
> error message. But understanding what is going on is a good first step:
> the
> automated solutions like fixatomorder will fail if there is some mistake in
> connectivity.
>
> ....dac
>
>
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--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
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Received on Mon May 03 2021 - 06:00:07 PDT
