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

From: David A Case <>
Date: Mon, 3 May 2021 08:26:05 -0400

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

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


AMBER mailing list
Received on Mon May 03 2021 - 05:30:05 PDT
Custom Search