[AMBER] Fwd: cpptraj issues

From: Thomas Pochapsky <pochapsk.brandeis.edu>
Date: Mon, 15 Aug 2016 11:02:22 -0400

If this helps, the .prmtop file in question was a legacy from AMBER 11,
but worked fine as input for AMBER 14 sander runs on multiple platforms.


-------- Forwarded Message --------
Subject: cpptraj issues
Date: Fri, 12 Aug 2016 12:52:19 -0400
From: Thomas Pochapsky <pochapsk.brandeis.edu>
To: AMBER Mailing List <amber.ambermd.org>

When attempting to load a .prmtop file into cpptraj, I get the following
error message:

Error: Atom 6415 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 MycGMIV.prmtop.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for MycGMIV.prmtop.

I tried 'fixatomorder", no difference.

If it helps, atom 6415 is the first K+ ion used to solvate and balance

Any suggestions?

Tom Pochapsky

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Received on Mon Aug 15 2016 - 08:30:02 PDT
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