Hi,
I have a fix for this issue in the works. It's a cpptraj command that
will re-order atoms in input coordinates when atom numbering inside
molecules is not sequential, as well as produce a fixed topology file.
I am currently testing it extensively and if it holds up it may be
released as an update, so sit tight.
If you could send me (off-list) your topology file and 1 or 2 frames
of coordinates that I could use for testing that would be great.
Thanks,
-Dan
On Thu, Jul 11, 2013 at 10:12 PM, Fabrício Bracht <fabracht1.gmail.com> wrote:
> 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)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 12 2013 - 09:30:03 PDT
