Hi,
You may want to try parmed from AmberTools 16 (or even the GitHub
version). There have been many improvements and fixes since Amber 14.
-Dan
On Mon, Jun 6, 2016 at 2:01 PM, Damiano Spadoni <enxds6.nottingham.ac.uk> wrote:
> Hello AMBERs,
>
> I've got a problem with a topology and coordinate files created by xleap.
>
> I used the .pdb file of a protein surrounded by 300 oxygen molecules to feed in xleap, then it's been neutralized and water solvent in an octahedral water box were added. Every checks during this procedure and the pleasant final NO RESTRAINTS reply to the command "saveamber parm .prmtop .inpcrd" let me believe everything was ok.
>
> The minimization stops with a warning that is related to such topology files and checking the validity on Parmed.Py, the following warning was received:
>
> ParmWarning: ATOMS_PER_MOLECULE section corrupt! Molecules are not contiguous!
>
> >From previous AMBERs suggestions, as this is a quite common problem, I typed:
>
>> setMolecules ATOMS_PER_MOLECULE=true
> Action setMolecules failed
> SeriousParmWarning: Value of solute_ions is unrecognized [ATOMS_PER_MOLECULE=true]! Assuming True
>
> even if I write:
>
>> setMolecules solute_ions=true
> Action setMolecules failed
> SeriousParmWarning: Value of solute_ions is unrecognized [solute_ions=true]! Assuming True
>
> Whilst if I simply type:
>
>> setMolecules
> Setting MOLECULE properties of the prmtop (SOLVENT_POINTERS and ATOMS_PER_MOLECULE)
> Traceback (most recent call last):
> File "/media/RAIDstorage/software/amber14/bin/parmed.py", line 159, in <module>
> parmed_commands.cmdloop()
> File "/usr/lib/python2.7/cmd.py", line 142, in cmdloop
> stop = self.onecmd(line)
> File "/usr/lib/python2.7/cmd.py", line 221, in onecmd
> return func(arg)
> File "<string>", line 1, in <lambda>
> File "/media/RAIDstorage/software/amber14/bin/ParmedTools/parmed_cmd.py", line 141, in _normaldo
> action.execute()
> File "/media/RAIDstorage/software/amber14/bin/ParmedTools/ParmedActions.py", line 974, in execute
> owner = self.parm.rediscover_molecules(self.solute_ions)
> AttributeError: 'setmolecules' object has no attribute 'solute_ions'
>
> And it automatically quits.
> Is there any way to fix those files?
> It can do that parmed.py or should I refer to something else?
>
> Any helps would be greatly appreciated.
>
> Damiano
>
>
>
>
>
>
>
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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
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Received on Mon Jun 06 2016 - 13:30:02 PDT
