VMD-L Mailing List
From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Sat Aug 17 2024 - 05:03:19 CDT
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Hi Daniel thank you for your kind update and I had inquired with the ORCA
Forum towards this modification and am simultaneously working
towards the same .inp C5-water interaction via a fragment of the ligand
precluding the adjacent carbon atom-water interaction, i'll update you
and forum regardless, thanks again:), Joel 🚀
On Sat, Aug 17, 2024 at 4:45 AM Daniel Fellner <dfel694_at_aucklanduni.ac.nz>
wrote:
> 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 🚀
>>>>>>>
>>>>>>
- Next message: Joel Subach: "Re: Re: flipping a .inp file for a water interaction INQUIRY"
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