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?
Thanks
Martin
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Received on Tue Jan 15 2019 - 11:00:03 PST
