Re: [AMBER] atom-order problem with prmtop and cpptraj

From: Vaibhav Dixit <>
Date: Mon, 3 May 2021 18:09:09 +0530

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
After fixing that all seems to be correct as shown by parmed >>
thanks for your suggestions.

On Mon, May 3, 2021 at 5:56 PM David A Case <> 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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> AMBER mailing list

Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
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Received on Mon May 03 2021 - 06:00:07 PDT
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