VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Sat May 11 2024 - 10:49:03 CDT

 I will `for now´ follow the ffTK Tutorial scripts i.e. without solvation
to maintain best CHARMM compatibility.

On Thu, May 9, 2024 at 12:04 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
wrote:

> image attached:
>
> On Wed, May 8, 2024 at 9:06 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
> wrote:
>
>> ...feel free to comment on my suggested solvation modifications below (I
>> am unsure if its formatted correctly and moreover if there are any
>> suggested modifications needed i.e. -D3 etc.), thanks:):
>>
>> Geometry Optimization: ! MP2 6-31G* TightSCF opt -->
>>
>> ! B3LYP 6-31G* TightSCF opt
>> !CPCM(Water)
>> %maxcore 4000
>>
>> %output
>> PrintLevel Mini
>> Print [ P_Mulliken ] 1
>> Print [ P_AtCharges_M ] 1
>> end
>>
>> %coords
>> CTyp xyz
>> Charge 0
>> Mult 1
>> Units Angs
>> coords
>>
>> N 111.38200378 109.63400269 61.88000107
>> N 105.40599823 107.05400085 60.49200058
>> ...
>> H 101.45600128 102.40799713 61.65399933
>> H 109.52500153 102.40299988 59.88899994
>> end
>> end
>>
>>
>> Water Interaction: ! HF 6-31G* TightSCF opt --->
>>
>> ! B3LYP 6-31G* TightSCF opt
>> !CPCM(Water)
>> %maxcore 1000
>>
>> %geom
>> ConnectFragments
>> { 1 2 O 9 66 }
>> end
>> Constraints
>> { B 9 66 C }
>> { D * 67 9 * C }
>> end
>> invertConstraints true
>> end
>>
>> %coords
>> CTyp xyz
>> Charge 0
>> Mult 1
>> Units Angs
>> coords
>>
>> N(1) 111.3489990234375 110.1510009765625 61.86199951171875
>> N(1) 106.43699645996094 106.68199920654297 61.29399871826172
>> ...
>> O(2) 108.47699737548828 112.79299926757812 61.159000396728516
>> H(2) 108.85800170898438 112.92400360107422 62.027000427246094
>> end
>> end
>>
>>
>> Calc. Bonded: ! MP2 6-31G* TightSCF opt NumFreq --->
>>
>> ! B3LYP 6-31G* TightSCF opt NumFreq
>> !CPCM(Water)
>> %maxcore 1000
>>
>> %geom
>> ConnectFragments
>> { 1 2 O 9 66 }
>> end
>> Constraints
>> { B 9 66 C }
>> { D * 67 9 * C }
>> end
>> invertConstraints true
>> end
>>
>> %coords
>> CTyp xyz
>> Charge 0
>> Mult 1
>> Units Angs
>> coords
>>
>> N(1) 111.3489990234375 110.1510009765625 61.86199951171875
>> N(1) 106.43699645996094 106.68199920654297 61.29399871826172
>> ...
>> O(2) 108.47699737548828 112.79299926757812 61.159000396728516
>> H(2) 108.85800170898438 112.92400360107422 62.027000427246094
>> end
>> end
>>
>> On Tue, May 7, 2024 at 8:33 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
>> wrote:
>>
>>> Hello VMD Community:),
>>>
>>> I wish to add an Implicit Solvation to my suggested CHARMM prerequisite
>>> compatible ffTK ORCA Methods outlined below:
>>>
>>> Geometry Optimization: ! MP2 6-31G* TightSCF opt
>>>
>>> Water Interaction: ! HF 6-31G* TightSCF opt
>>>
>>> Calc. Bonded: ! MP2 6-31G* TightSCF opt NumFreq
>>>
>>> Only experts have been recommended to modify the above ffTK suggested
>>> methods since the HF/6-31G(d) level of theory needs to be maintained
>>> towards consistency with the CHARMM force field. After reading the ORCA
>>> Manual Implicit Solvation Section I still find this modification towards
>>> implicit solvation to be beyond the scope of my expertise for best results.
>>> Accordingly if you have any suggestion towards modifying my above input
>>> files towards ORCA execution to generate best solvent exposed calculations
>>> that would yet still be CHARMM compatible to their above methods feel free
>>> to make a suggestion(s) . (The ffTK literature and tutorial do not exhibit
>>> this expertise.). Thanks if you know:).
>>>
>>> Joel[image: 🚀]
>>>
>>