Hi, what’s exact command have you tried?
Hai
On Fri, Jun 24, 2022 at 10:15 AM EMANUELE CASALI <
emanuele.casali01.universitadipavia.it> wrote:
> Dear Hai Nguyen,
> I tried your suggestion, but I got the followings:
>
> Unexpected failure:
> AttributeError: 'str' object has no attribute 'decode'
>
> Traceback is
>
> File
> "/opt/amber20/lib/python3.9/site-packages/parmed/tools/parmed_cmd.py", line
> 161, in _normaldo
> action.execute()
> File "/opt/amber20/lib/python3.9/site-packages/parmed/tools/actions.py",
> line 4190, in execute
> san_min(self.parm, self.igb, self.saltcon, self.cutoff, self.tol,
> File
> "/opt/amber20/lib/python3.9/site-packages/parmed/tools/simulations/sanderapi.py",
> line 142, in minimize
> results.message.decode())
>
> Emanuele
>
> Il giorno ven 24 giu 2022 alle ore 15:01 Hai Nguyen <nhai.qn.gmail.com>
> ha scritto:
>
>>
>>
>> On Fri, Jun 24, 2022 at 4:54 AM EMANUELE CASALI via AMBER <
>> amber.ambermd.org> wrote:
>>
>>> Dear all,
>>> I am contacting you since we found some issue running parmed under
>>> Amber20
>>> installat. Namely, the minimize function ends always up with the error:
>>> Unexpected failure:
>>> TypeError: '>=' not supported between instances of 'int' and 'NoneType'
>>>
>>> Traceback is
>>>
>>> File
>>> "/opt/amber20/lib/python3.9/site-packages/parmed/tools/parmed_cmd.py",
>>> line
>>> 161, in _normaldo
>>> action.execute()
>>> File
>>> "/opt/amber20/lib/python3.9/site-packages/parmed/tools/actions.py",
>>> line 4190, in execute
>>> san_min(self.parm, self.igb, self.saltcon, self.cutoff, self.tol,
>>> File
>>>
>>> "/opt/amber20/lib/python3.9/site-packages/parmed/tools/simulations/sanderapi.py",
>>> line 135, in minimize
>>> results = optimize.minimize(energy_function, parm.coordinates,
>>> File
>>>
>>> "/opt/amber20/miniconda/lib/python3.9/site-packages/scipy/optimize/_minimize.py",
>>> line 623, in minimize
>>> return _minimize_lbfgsb(fun, x0, args, jac, bounds,
>>> File
>>>
>>> "/opt/amber20/miniconda/lib/python3.9/site-packages/scipy/optimize/lbfgsb.py",
>>> line 367, in _minimize_lbfgsb
>>> if n_iterations >= maxiter:
>>>
>>>
>> Hi,
>> Try to set maxcyc to a number. The default value is None.
>>
>> https://github.com/ParmEd/ParmEd/blob/b9f2955f792c03394686824519cabe030d5342b4/parmed/tools/actions.py#L3920-L3922
>>
>> Hai
>>
>>
>>> I hope you can help us finding a solution to fix the issue.
>>> Many thanks in advance
>>> Emanuele
>>>
>>> --
>>> *Emanuele Casali, Ph. D.*
>>> Postdoctoral Research Fellow
>>> University of Pavia
>>> Department of Chemistry
>>> Viale Taramelli, 10
>>> 27100 Pavia - Italy
>>>
>>> Phone: +39 3409133834
>>> e-mail: emanuele.casali01.universitadipavia.it
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>
> --
> *Emanuele Casali, Ph. D.*
> Postdoctoral Research Fellow
> University of Pavia
> Department of Chemistry
> Viale Taramelli, 10
> 27100 Pavia - Italy
>
> Phone: +39 3409133834
> e-mail: emanuele.casali01.universitadipavia.it
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 04 2022 - 13:33:09 PDT
