[AMBER] Fwd: cpptraj issues

From: Thomas Pochapsky <pochapsk.brandeis.edu>
Date: Tue, 16 Aug 2016 10:20:30 -0400

I think I answered my own question, but for the record, the .mdcrd files
generated by sander (AMBER14) need a blank line at the top of the file
to be read correctly using trajin, at least with a .prmtop of older
vintage. We found this to be true if you want to import .mdcrd files as
.trj files into PyMOL as well.

-------- 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 Tue Aug 16 2016 - 07:30:03 PDT
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