VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Fri Aug 16 2024 - 21:45:53 CDT

Sorry, I don't recognise the format of the input file. I've only used
Gaussian.

I'm guessing something in this part should be changed:

%geom
> ConnectFragments
> { 1 2 O 6 66 }
> end
> Constraints
> { B 6 66 C }
> { D * 67 6 * C }
> end
> invertConstraints true
> end

This is what it looks like for Gaussian, the value to change is higlighted
in red:

H1w C23 rAH C15 90.66 O24 *91.21*
> x H1w 1.0 C23 90.00 C15 0.00
> Ow H1w 0.9572 x 90.00 C23 180.00
> H2w Ow 0.9572 H1w 104.52 x dih

rAH 2.0
> dih 0.0

*Daniel Fellner BSc(Hons)*
PhD Candidate | Research Assistant
School of Chemical Sciences
University of Auckland
Ph +64211605326

On Sun, 4 Aug 2024 at 23:11, Joel Subach <mjsubach_at_alumni.ncsu.edu> wrote:

> *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 🚀
>>>>>>
>>>>>