VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Sat Nov 09 2024 - 23:39:54 CST

Hello VMD Forum:).

Because my .inp file is not in Z-Matrix Format I instead had flipped the
water molecule to the other side of the ligand via the below
Avogadro Forum entitled below: (I had inquired to the VMD Administration
etc. if sharing this below solution is allowed but did not
receive a response, accordingly if not feel free to request this deletion),
thanks:), Joel [image: 🚀]

Flipping a Waters Coordinates to the other Side of a Ligand Inquiry?

On Sun, Aug 18, 2024 at 11:47 AM Joel Subach <mjsubach_at_alumni.ncsu.edu>
wrote:

> ...and Daniel I ffTK generated the Gaussian input file which exhibits the
> dihedral needing the modification,
> accordingly if you would know how to regenerate this .gau file to an ORCA
> .inp file subsequent to the degree
> modification feel free to update me accordingly, see paste below and
> attached, thanks if you know:), Joel
>
> %chk=14C-ACC-C5.chk
> %nproc=1
> %mem=1GB
> # HF/6-31G* Opt=(Z-matrix,MaxCycles=100) Geom=PrintInputOrient
>
> <qmtool> simtype="Geometry optimization" </qmtool>
> 14C-ACC-C5
>
> 0 1
> N1 111.3489990234375 110.1510009765625 61.86199951171875
> N2 106.43699645996094 106.68199920654297 61.29399871826172
> C3 110.01799774169922 109.9229965209961 61.590999603271484
> C4 109.39399719238281 109.42900085449219 62.775001525878906
> C5 107.40599822998047 109.0989990234375 61.492000579833984
> C6 108.05599975585938 108.99800109863281 62.71500015258789
> C7 111.58399963378906 109.78700256347656 63.18000030517578
> C8 112.3290023803711 110.26799774169922 60.78200149536133
> C9 110.4010009765625 109.36699676513672 63.775001525878906
> C10 109.33100128173828 110.0719985961914 60.37699890136719
> C11 105.52200317382812 105.63999938964844 61.81399917602539
> C12 107.18199920654297 106.31099700927734 60.084999084472656
> C13 108.00900268554688 109.6520004272461 60.3390007019043
> C14 112.28500366210938 109.05400085449219 59.874000549316406
> C15 104.43399810791016 105.23699951171875 60.854000091552734
> C16 108.29199981689453 105.3479995727539 60.439998626708984
> C17 112.89299774169922 109.94999694824219 63.82699966430664
> C18 111.86100006103516 107.80699920654297 60.349998474121094
> C19 112.68299865722656 109.1719970703125 58.53499984741211
> C20 103.25800323486328 105.99700164794922 60.75899887084961
> C21 109.04000091552734 105.53700256347656 61.611000061035156
> C22 104.59500122070312 104.12000274658203 60.02299880981445
> C23 108.62300109863281 104.29000091552734 59.58100128173828
> C24 111.8030014038086 106.7040023803711 59.49800109863281
> C25 112.6500015258789 108.06900024414062 57.683998107910156
> C26 112.19100189208984 106.83300018310547 58.15700149536133
> C27 102.26399993896484 105.64399719238281 59.845001220703125
> C28 110.08300018310547 104.66400146484375 61.93199920654297
> C29 103.5989990234375 103.76599884033203 59.106998443603516
> C30 109.67500305175781 103.41999816894531 59.89699935913086
> C31 102.43399810791016 104.53099822998047 59.01499938964844
> C32 110.40699768066406 103.6050033569336 61.07500076293945
> C33 112.1729965209961 105.68399810791016 57.19599914550781
> O34 105.05999755859375 108.38899993896484 62.54199981689453
> O35 105.2770004272461 108.66000366210938 60.01300048828125
> O36 112.87000274658203 109.46099853515625 65.09400177001953
> O37 113.89299774169922 110.45700073242188 63.33100128173828
> O38 111.33599853515625 104.6510009765625 57.4900016784668
> O39 112.86000061035156 105.6510009765625 56.19200134277344
> S40 105.84700012207031 108.26599884033203 61.30799865722656
> H41 113.76699829101562 109.62799835205078 65.4520034790039
> H42 110.76799774169922 104.86900329589844 58.255001068115234
> H43 107.5479965209961 108.57099914550781 63.577999114990234
> H44 113.30899810791016 110.40399932861328 61.242000579833984
> H45 112.10299682617188 111.1780014038086 60.21200180053711
> H46 110.29499816894531 109.07499694824219 64.81199645996094
> H47 109.81300354003906 110.46700286865234 59.48699951171875
> H48 105.10600280761719 106.01899719238281 62.750999450683594
> H49 106.16300201416016 104.78199768066406 62.053001403808594
> H50 107.62100219726562 107.21900177001953 59.65800094604492
> H51 106.51899719238281 105.88300323486328 59.32099914550781
> H52 107.4209976196289 109.73799896240234 59.42900085449219
> H53 111.55500030517578 107.68900299072266 61.38800048828125
> H54 113.01399993896484 110.13600158691406 58.152000427246094
> H55 103.125 106.86199951171875 61.40599822998047
> H56 108.78199768066406 106.35900115966797 62.27399826049805
> H57 105.4990005493164 103.51599884033203 60.10499954223633
> H58 108.04000091552734 104.12899780273438 58.67499923706055
> H59 111.48600006103516 105.74800109863281 59.90700149536133
> H60 112.96499633789062 108.14900207519531 56.64699935913086
> H61 101.35600280761719 106.23799896240234 59.779998779296875
> H62 110.64700317382812 104.81099700927734 62.85100173950195
> H63 103.73200225830078 102.8949966430664 58.46900177001953
> H64 109.91500091552734 102.59600067138672 59.229000091552734
> H65 101.65699768066406 104.25800323486328 58.30400085449219
> H66 111.21399688720703 102.9209976196289 61.327999114990234
> H1w C7 rAH N1 91.40 C9 92.00
> x H1w 1.0 C7 90.00 N1 0.00
> Ow H1w 0.9572 x 90.00 C7 180.00
> H2w Ow 0.9572 H1w 104.52 x dih
>
> rAH 2.0
> dih 0.0
>
> On Sat, Aug 17, 2024 at 12:03 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
> wrote:
>
>> 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 🚀
>>>>>>>>>
>>>>>>>>