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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Received on Mon Jun 06 2016 - 13:30:02 PDT
