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From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Sun Aug 04 2024 - 05:04:33 CDT
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..and the Z-Matrix rightmost value is the dihedral not a coordinate,
accordingly disregard my initial Z-Matriz value reply
On Sat, Aug 3, 2024 at 11:45 AM Joel Subach <mjsubach_at_alumni.ncsu.edu>
wrote:
> ...and attached is my .inp and output.out files in case you would need to
> inspect them to discover where to find these values:
>
> Thanks if you can:)
>
> On Sat, Aug 3, 2024 at 10:22 AM Joel Subach <mjsubach_at_alumni.ncsu.edu>
> wrote:
>
>> Hi Daniel thank you for your kind update:).
>>
>> My ffTK generated .inp file only exhibits Cartesian Coordinates, however,
>> the ffTK generated .out file exhibits the Z-Matrices.
>>
>> I had went into both files regardless and changed the final water
>> coordinate numerical values adding +90 and subtracting -90 (adding +90 and
>> -90 to the .inp existing water cartesian coordinates 62.65, 62.40, 61.45)
>> and similarly for the final values in the Z-Matrix exhibited within the
>> output.out files final Z-Matriz values (adding +90 and -90 to the .out
>> existing Z-Matriz 243.05, 285.27, 203.00), when subsequently viewing
>> each via Pymol the new water molecule was very very far from the desired
>> flip (see-attached screenshot of the .inp and .out files exhibiting
>> the cartesian and Z-Matrix values).
>>
>> I will probably need a more detailed explanation since my understanding
>> in how to adjust these coordinates may lack the experience needed.
>>
>> Thanks if you have the time:)
>>
>> On Fri, Aug 2, 2024 at 3:50 AM Daniel Fellner <dfel694_at_aucklanduni.ac.nz>
>> wrote:
>>
>>> Hi Joel,
>>>
>>> Sometimes FFTK generates the Z-matrix with a slightly different format,
>>> so it depends on the specific way your input files have it specified.
>>>
>>> Usually it's the right-most value in the first row, but I'm not sure if
>>> this is for donors or acceptors.
>>>
>>> In any case, try changing any of the values that are approx. 90 degrees,
>>> to their opposite (e.g. -90.1 to +89.9) and see what effect it has. You
>>> should only need to change one of the values to cause it to flip.
>>>
>>>
>>> *Daniel Fellner BSc(Hons)*
>>> PhD Candidate | Research Assistant
>>> School of Chemical Sciences
>>> University of Auckland
>>> Ph +64211605326
>>>
>>>
>>> On Fri, 2 Aug 2024 at 05:08, Joel Subach <mjsubach_at_alumni.ncsu.edu>
>>> wrote:
>>>
>>>> Hello Daniel, I hope you're well:).
>>>>
>>>> I had posted this first inquiry within the VMD Forum without success
>>>> and had read your assistance to Emma via the next below link:
>>>>
>>>>
>>>> *https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/34666.html
>>>> <https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/34666.html>*
>>>>
>>>>
>>>> *https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32204.html
>>>> <https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32204.html>*
>>>>
>>>> If you could assist by being more specific towards my flip it would be
>>>> very helpful.
>>>>
>>>> Thanks if you know:),
>>>> Joel 🚀
>>>>
>>>
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