On Wed, Mar 8, 2023 at 3:29 AM maryam ghorbaninia <marygh72.gmail.com>
wrote:
> Hi,
>
> With these topology and trajectory files, I performed my analysis by
> CPPTRAJ.
>
> Yes, my files exist and they are not empty files.
>
Can you please try again with another pdb file?
I can’t think of any reason.
Hai
>
> I found the same error here :
>
>
> https://github.com/insilichem/utils/blob/main/convergence_analysis_MD_pytraj.ipynb
>
> Thanks,
> Maryam
>
>
>
> On Fri, Mar 3, 2023, 15:36 maryam ghorbaninia <marygh72.gmail.com> wrote:
>
>> Hi,
>>
>> With these topology and trajectory files, I performed my analysis by
>> CPPTRAJ.
>>
>> Yes, my files exist and they are not empty files.
>>
>> I found the same error here :
>>
>>
>> https://github.com/insilichem/utils/blob/main/convergence_analysis_MD_pytraj.ipynb
>>
>> Thanks,
>> Maryam
>>
>>
>> Hai Nguyen via AMBER <amber.ambermd.org> در تاریخ پنجشنبه ۲ مارس
>> ۲۰۲۳ ساعت ۲۲:۴۷ نوشت:
>>
>>> On Thu, Mar 2, 2023 at 2:05 PM maryam ghorbaninia via AMBER <
>>> amber.ambermd.org> wrote:
>>>
>>> > Hi,
>>> > In pytraj I cannot load my files.
>>> > my scripts were:
>>> >
>>> > *traj = pt.iterload('my-file.nc <http://my-file.nc>',
>>> 'my-file.parm7')*
>>> > or
>>> > *pt.iterload('my_file.pdb')*
>>> >
>>> >
>>> Hi
>>>
>>> Is this my_file.pdb legit? (e.g: does it exist? is it an empty file?)
>>>
>>> Hai
>>>
>>> and I got this error on both:
>>> >
>>> > *RuntimeError: n_atoms = 0: make sure to load correct Topology
>>> filename or
>>> > load supported topology (pdb, amber parm, psf, ...)*
>>> >
>>> > I would be grateful if you help me.
>>> >
>>> > Best,
>>> > Maryam
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >
>>> _______________________________________________
>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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Received on Wed Mar 08 2023 - 10:00:03 PST
