On Tue, Aug 16, 2016 at 8:20 AM, Thomas Pochapsky <pochapsk.brandeis.edu> wrote:
> 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.
This is because the Amber ASCII trajectory format requires a title
line (see
http://ambermd.org/formats.html#trajectory).
I'm not clear on how you got a trajectory file with no title (perhaps
you used the '-A' command line flag with a non-existent trajectory
file?) or how adding a title to your trajectory file would fix a
topology with molecules having non-contiguous atoms.
-Dan
>
>
>
> -------- 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
> charge.
>
> Any suggestions?
>
> Thanks,
> Tom Pochapsky
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Aug 16 2016 - 08:00:06 PDT
