Re: [AMBER] Autoimage command not working

From: Premila Samuel Mohan Dass <>
Date: Tue, 15 Jan 2019 18:50:47 +0000

I used to get the same problem. Make sure your heme for each chain follows the chain right after when you set up the system with leap to create bond between HID and FE. I assume you are working on hemoglobin


On Jan 15, 2019, at 1:40 PM, Martín Pettinati <<>> wrote:

Dear Amber users

I'm running molecular dynamics on a tetrameric hemeprotein. In order to run the simulation I set for every subunit a bond between one HID residue and the Fe atom. I don't encounter any errors while running tleap nor the simulation. But when I try to load the trayectories into cpptraj and run the "autoimage" command I encounter this:

Error: Atom 8769 was assigned a lower molecule # than previous atom.
Error: This can happen if bond information is incorrect or missing, or if the
Error: atom numbering in molecules is not sequential. Try one of the
Error: following:
Error: - If this is a PDB file, try using the 'noconect' keyword.
Error: - If this topology did not have bond info, try increasing the bond
Error: search cutoff above 0.2 Ang. ('bondsearch <cutoff>').
Error: - Use the 'fixatomorder' command to reorder the topology and any
Error: associated coordinates.
Error: - Use the 'setMolecules' command in parmed to reorder only the
Error: topology.
Error: Could not determine molecule information for HEM.prmtop.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for HEM.prmtop.

 0: [autoimage]
Warning: Topology HEM.prmtop does not contain molecule information
Warning: Setup incomplete for [autoimage]: Skipping

Autoimage is not performed. I tried running the "fixatomorder" command and exporting a new topology file but it didn't work.

Any suggestions?



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Received on Tue Jan 15 2019 - 11:00:04 PST
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