From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Sat Oct 21 2023 - 07:09:38 CDT

Hello JC thank you for your kind update:).

I had modified my par_all36_cgenff.prm improper to:

CG2O2 CG2R51 OG2D1 OG311 53.0000 0 0.00 ! IMPOROPER PARAMETER
ERROR

which were the values in my .str file generated via CGenff (this was
suggested in lieu of a zero value via an ORCA Memberr
and makes sense since it was in my .str file)

but this time I also updated my previous parameter file via the generated
Scan Torsions Tab and added the par_all36_cgenff.prm
as well as my .par file to the Input Parameter Files Section within the Opt
Torsions Tab (it states to add both the predefined and in progress
parameter files) last times I only added the .par file so yes JC good
intuition since my amendment was within this par_all36_cgenff.prm file 👌.

Best,
Joel 🚀

On Fri, Oct 20, 2023 at 11:45 PM Gumbart, JC <gumbart_at_physics.gatech.edu>
wrote:

> Are you sure it’s reading the right file? i.e., is this the file that you
> give to FFTK? Like Josh says, it looks okay to me. Sometimes I find a
> second set of eyes helps me discover obvious errors I’m overlooking; maybe
> ask someone else there to take a look at what you’re doing step by step.
>
> FFTK can create debugging logs; maybe try that to see if you can track
> down the disconnect.
>
> Best,
> JC
>
> On Oct 20, 2023, at 10:39 AM, Joel Subach <mjsubach_at_alumni.ncsu.edu>
> wrote:
>
> Hello Josh thank you for your kind update:).
>
> I added:
>
> IMPROPERS
> CG2O2 CG2R51 OG2D1 OG311 53.0000 0 0.00 !
>
> to my par_all36_cgenff.prm file and generated the same error (see-thread)
>
> and also tried adding:
>
> IMPROPERS
> CG2O2 CG2R51 OG2D1 OG311 0.0000 0 0.00 !
>
> to my par_all36_cgenff.prm file and generated the same error.
>
> I skipped the Opt Charges and other tabs and jumped right to the dihedral
> angle optimization last two-tabs,
> maybe I need to sequentially go through each tab updating the
> parameter file along the way to resolve this?
> (I only need to optiimze two dihedral angles.)
>
> Thanks if you know:)
> Joel 🚀
>
>
> On Fri, Oct 20, 2023 at 4:32 PM Josh <vermaasj_at_msu.edu> wrote:
>
>> Hi Joel,
>>
>> You *did* add the new parameter file you made to your namd configuration
>> file, right? This looks like it should have worked to me.
>>
>> -Josh
>>
>> On 10/20/23 10:19 AM, Joel Subach wrote:
>>
>> ...hi and I updated the missing values to:
>>
>> IMPROPERS
>> CG2O2 CG2R51 OG2D1 OG311 53.0000 0 0.00 !
>>
>> which were the values generated via CGenff in my .str file and the same
>> Fatal Error:
>>
>> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2O2 CG2R51 OG2D1
>> OG311 (ATOMS 17 7 37 36)
>> [Partition 0][Node 0] End of program
>>
>> (the input of a zaro value did not function and gave the sae error)
>>
>> I will try and start all over updating my parameter files while
>> additionally using the partial charges tab, maybe this may repair this
>> error, if you think of another way feel free to update me accordingly,
>> thanks:)
>>
>> <https://urldefense.com/v3/__https://orcaforum.kofo.mpg.de/ucp.php?i=pm&mode=view&f=-2&p=2452*top__;Iw!!HXCxUKc!yIklqDtdzlcrx38jVlCoktFkWkrj7pHAbGfsypWihTjYHHF4zeTxLs5Pa9pj8K0RTjtBGC6XjzZtRlloomoeWL8$>
>>
>>
>> On Sun, Oct 15, 2023 at 9:56 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
>> wrote:
>>
>>> ...and I did generate the DihOpt.log file regardless of the FATAL_ERROR
>>> (see--log file attached) although
>>> I am unsure if the FATAL-ERROR needs to be resolved first
>>> before proceeding? Thanks:)
>>>
>>> On Sun, Oct 15, 2023 at 8:29 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
>>> wrote:
>>>
>>>> ...and is this error possibly being generated via my .prm file not
>>>> being filled out completely i.e. missing the ! and words?
>>>> (See attached screenshot exhibiting the error file in the top right
>>>> corner and the amended .prm file highlighted in center.)
>>>>
>>>> On Sun, Oct 15, 2023 at 6:49 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
>>>> wrote:
>>>>
>>>>> Hello JC thank you for your kind update:) and I changed the 0 to a O
>>>>> and precipitated the same error,
>>>>> please see screenshot attached exhibiting this error and its attached
>>>>> log.file in detail. Thanks if you have
>>>>> a resolution to this problem:).
>>>>>
>>>>> On Sun, Oct 15, 2023 at 6:19 PM Gumbart, JC <
>>>>> gumbart_at_physics.gatech.edu> wrote:
>>>>>
>>>>>> I believe that should be CG2O2, not CG202 (the letter O, not the
>>>>>> number 0). It can be hard to tell sometimes!
>>>>>>
>>>>>> Best,
>>>>>> JC
>>>>>>
>>>>>> On Oct 15, 2023, at 12:01 PM, Joel Subach <mjsubach_at_alumni.ncsu.edu>
>>>>>> wrote:
>>>>>>
>>>>>> Hello Josh thank you for your kind update:).
>>>>>>
>>>>>> I amended, as you had recommended, the .prm file generated during my
>>>>>> initial ffTK run and precipitated the same error
>>>>>> (see screenshot attached labeled FATAL ERROR where at the top-right
>>>>>> you can read the error and the bottom right
>>>>>> exhibits my modified .prm file as recommended, on the left is the OPT
>>>>>> Torsion GUI. Also attached is the complete error-
>>>>>> log file for your inspection. Thanks if you can help:)
>>>>>>
>>>>>> Best,
>>>>>> Joel 🚀
>>>>>>
>>>>>> On Sat, Oct 14, 2023 at 7:15 PM Vermaas, Josh <vermaasj_at_msu.edu>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Joel,
>>>>>>>
>>>>>>> Take a look at par_all36m_prot.prm from the standard CHARMM
>>>>>>> parameter file. There will be an improper section that you can crib from. A
>>>>>>> typical line will look something like this:
>>>>>>>
>>>>>>> HR1 NR1 NR2 CPH2 0.5000 0 0.0000
>>>>>>>
>>>>>>> You'd change the 4 atomtypes to be what you need them to be for your
>>>>>>> system, and then make the 0.5 (the force constant for the improper energy)
>>>>>>> 0.
>>>>>>>
>>>>>>> -Josh
>>>>>>>
>>>>>>> On 10/14/23, 11:37 AM, "owner-vmd-l_at_ks.uiuc.edu <mailto:
>>>>>>> owner-vmd-l_at_ks.uiuc.edu> on behalf of Joel Subach" <
>>>>>>> owner-vmd-l_at_ks.uiuc.edu <mailto:owner-vmd-l_at_ks.uiuc.edu> on behalf
>>>>>>> of mjsubach_at_alumni.ncsu.edu <mailto:mjsubach_at_alumni.ncsu.edu>>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>> Hello JC thank you so much for teaching me via your kind update:).
>>>>>>>
>>>>>>>
>>>>>>> Can you please be more specific in this modification since I have
>>>>>>> never
>>>>>>> done this before, below is my .par existing file:
>>>>>>>
>>>>>>>
>>>>>>> IMPROPER
>>>>>>> !
>>>>>>> !V(improper) = Kpsi(psi - psi0)**2
>>>>>>> !
>>>>>>> !Kpsi: kcal/mole/rad**2
>>>>>>> !psi0: degrees
>>>>>>> !note that the second column of numbers (0) is ignored
>>>>>>> !
>>>>>>> !atom types Kpsi psi0
>>>>>>> !
>>>>>>>
>>>>>>>
>>>>>>> i.e. how would you suggest to modify the above i.e. add the dummy
>>>>>>> improper
>>>>>>> with a force constant of zero?
>>>>>>>
>>>>>>>
>>>>>>> Thanks if you can:)
>>>>>>> Joel 🚀
>>>>>>>
>>>>>>>
>>>>>>> On Sat, Oct 14, 2023 at 4:49 AM Gumbart, JC <
>>>>>>> gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>> > Hi Joel,
>>>>>>> >
>>>>>>> > You could just manually add a dummy improper with a force constant
>>>>>>> of zero
>>>>>>> > for now. You can then optimize the improper after getting the
>>>>>>> dihedrals.
>>>>>>> >
>>>>>>> > Best,
>>>>>>> > JC
>>>>>>> >
>>>>>>> > On Oct 13, 2023, at 7:52 AM, Joel Subach <mjsubach_at_alumni.ncsu.edu
>>>>>>> <mailto:mjsubach_at_alumni.ncsu.edu>> wrote:
>>>>>>> >
>>>>>>> > Hello VMD Community, towards the above topic:
>>>>>>> >
>>>>>>> > Via the ffTK Opt Torsions Tab to optimize dihedral parameters
>>>>>>> (Tutorial 6.2
>>>>>>> > link: *
>>>>>>> https://urldefense.com/v3/__https://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf__;!!HXCxUKc!289sVcRC0LJsy6eLNdZulE3nAygnHtJ2rH5Ls5vYnhLoXVPaUpEEjUYVYPZuAZxM3SAQQUw0HOvQynGndo7mdnw$
>>>>>>> <
>>>>>>> https://urldefense.com/v3/__https://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf__;!!HXCxUKc!289sVcRC0LJsy6eLNdZulE3nAygnHtJ2rH5Ls5vYnhLoXVPaUpEEjUYVYPZuAZxM3SAQQUw0HOvQynGndo7mdnw$>
>>>>>>>
>>>>>>> > <
>>>>>>> https://urldefense.com/v3/__https://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf__;!!HXCxUKc!289sVcRC0LJsy6eLNdZulE3nAygnHtJ2rH5Ls5vYnhLoXVPaUpEEjUYVYPZuAZxM3SAQQUw0HOvQynGndo7mdnw$
>>>>>>> <
>>>>>>> https://urldefense.com/v3/__https://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf__;!!HXCxUKc!289sVcRC0LJsy6eLNdZulE3nAygnHtJ2rH5Ls5vYnhLoXVPaUpEEjUYVYPZuAZxM3SAQQUw0HOvQynGndo7mdnw$>
>>>>>>> >).*
>>>>>>> >
>>>>>>> > I had clicked Run Optimization after inputting:
>>>>>>> >
>>>>>>> > all of the proper files i.e. psf, pdb, par for the *input section *
>>>>>>> >
>>>>>>> > my 4-output.out resulting files generated via ORCA for the *QM
>>>>>>> Target
>>>>>>> > Data Section*
>>>>>>> >
>>>>>>> > and my atom types for my two-dihedral angles for the *Dihedral
>>>>>>> Parameter
>>>>>>> > Settings*
>>>>>>> >
>>>>>>> > the below error states:
>>>>>>> > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2O2 CG2R51
>>>>>>> OG2D1
>>>>>>> > OG311 (ATOMS 17 7 37 36)
>>>>>>> > [Partition 0][Node 0] End of program
>>>>>>> > FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2O2 CG2R51
>>>>>>> OG2D1
>>>>>>> > OG311 (ATOMS 17 7 37 36)
>>>>>>> >
>>>>>>> > (See complete Application_Error.log file attached and note within
>>>>>>> it the: *Info:
>>>>>>> > 0 IMPROPER*
>>>>>>> > may have been generated via ffTK?)
>>>>>>> >
>>>>>>> > Below is a paste of the impropers from my generated .par file:
>>>>>>> >
>>>>>>> > IMPROPER
>>>>>>> > !
>>>>>>> > !V(improper) = Kpsi(psi - psi0)**2
>>>>>>> > !
>>>>>>> > !Kpsi: kcal/mole/rad**2
>>>>>>> > !psi0: degrees
>>>>>>> > !note that the second column of numbers (0) is ignored
>>>>>>> > !
>>>>>>> > !atom types Kpsi psi0
>>>>>>> > !
>>>>>>> >
>>>>>>> > * Note i skipped to Scan Torsions since that was all I needed
>>>>>>> amended i.e
>>>>>>>
>>>>>>> <FATAL_ERROR.png><SAVE_TO_LOG.log>
>>>>>>
>>>>>>
>>>>>>
>> --
>> Josh Vermaas
>> vermaasj_at_msu.edu
>> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
>> Michigan State Universityvermaaslab.github.io
>>
>>
>