From: Anna Cebrian Prats <Anna.Cebrian.uab.cat>
Date: Thu, 21 Jul 2016 10:30:20 +0000

Good morning

I have used cpptraj to check the topology and the coordinates looks a like in a pdb

and at the beginning of the process with this command : cpptraj 3hs5-Fe-O-ph.top

I have obtained this error. What does it means? My topology is created wrong?

How can I solved? I already check in the manual and with a tutorial and suggest that the problem is with the atom order. However, I have been renumbered by the pdb4amber. Also can be that the bond is not defined but the frcmod file contains such information

CPPTRAJ: Trajectory Analysis. V15.00
    ___ ___ ___ ___
     | \/ | \/ | \/ |

| Date/time: 07/21/16 11:31:10
| Available memory: 825.504 MB

    Reading '3hs5-Fe-O-ph.top' as Amber Topology
Error: Atom 8915 was assigned a lower molecule # than previous atom. This can
Error: happen if 1) bond information is incorrect or missing, or 2) if the
Error: atom numbering in molecules is not sequential. If topology did not
Error: originally contain bond info, 1) can potentially be fixed by
Error: increasing the bondsearch cutoff offset (currently 0.200). 2) can be
Error: fixed by either using the 'fixatomorder' command, or using
Error: the 'setMolecules' command in parmed.py.
Error: Could not determine molecule information for 3hs5-Fe-O-ph.top.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for 3hs5-Fe-O-ph.top.
    Loading previous history from log 'cpptraj.log'

Thank you in advanced for your help

Kind regards


AMBER mailing list
Received on Thu Jul 21 2016 - 04:00:03 PDT
Custom Search