VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Fri Oct 20 2023 - 09:19:14 CDT

..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!!DZ3fjg!9EMAq73s-5yS2xZMnaJY7htbw8F7F1TlsWzGmEhgzpJcCTHIiIvaUxxl1qG7cwFZq3zJjY_bYhRXuxyr9tgxIiacNQ$ >

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>
>>>>
>>>>
>>>>