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
Anna
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Received on Thu Jul 21 2016 - 04:00:03 PDT
