VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Sun Aug 18 2024 - 04:47:22 CDT

..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 🚀
>>>>>>>>
>>>>>>>