Sure thing.
Error: Atom 5311 was assigned a lower molecule # than previous atom.
Error: This can happen if bond information is incorrect or missing.
Error: Detected # of molecules is 7615. If this is incorrect and your
Error: topology does not have bond information (e.g. PDB file), try
Error: increasing the bond search cutoff offset (currently 0.200000).
Error: e.g. 'parm HOH_wat.prmtop bondsearch <new offset>'.
Error: This can also happen if the atoms in your molecules are not
Error: sequential (e.g. molecule 1 is atoms 1-4,10-14 and molecule 2
Error: is atoms 5-9,15-20). This can be fixed using the 'setMolecules'
Error: command in parmed.py.
Error: could not determine molecule information for HOH_wat.prmtop.
Error: SetSolventInfo: No molecule information.
Error: could not determine solvent information for HOH_wat.prmtop.
Then I get, for example:
Warning: autoimage: Parm HOH_wat.prmtop does not contain molecule
information
2013/7/12 Daniel Roe <daniel.r.roe.gmail.com>
> Hi,
>
> On Thu, Jul 11, 2013 at 9:55 PM, Fabrício Bracht <fabracht1.gmail.com>
> wrote:
> > correct. All the simulations ran fine. The problem is, for example, the
> > closest command for cpptraj does not work. It worked fine with ambertools
> > 12, but now, with all the error check routines of ambertools 13 I'll have
>
> Could you post exactly the error you are getting from cpptraj? Thanks.
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
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> AMBER.ambermd.org
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>
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Received on Thu Jul 11 2013 - 21:30:05 PDT
