From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Sun Aug 04 2024 - 06:10:59 CDT

*wrong dihedral I meant i.e. maybe I need to create the proper dihderal, I
dont know

On Sun, Aug 4, 2024 at 12:04 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
wrote:

> ...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 🚀
>>>>>
>>>>