Did you see my previous response? The 'fixatomorder' command fixes the
coordinates internally - if you want a fixed (i.e. re-ordered)
topology and coordinates you will have to use the 'outprefix' keyword
with 'fixatomorder' and write out the re-ordered coordinates with a
'trajout' command.
On Mon, Aug 15, 2016 at 9:02 AM, Thomas Pochapsky <pochapsk.brandeis.edu> wrote:
> 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.
You can still run MD with these topologies, off the top of my head I
don't think there are any adverse effects (maybe some small artifacts
with pressure scaling when running NTP?). The re-ordering is important
for analysis since many commands in cpptraj require that atoms in
molecules have contiguous numbering.
-Dan
>
> TCP
>
>
>
> -------- 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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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 Mon Aug 15 2016 - 11:00:02 PDT
