VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Fri Oct 20 2023 - 09:39:13 CDT

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
>
>