VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Fri Oct 20 2023 - 16:45:25 CDT

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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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> <mailto: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> <mailto: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> <mailto: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> <mailto: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> <mailto: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<mailto:vermaasj_at_msu.edu>
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io<https://urldefense.com/v3/__http://vermaaslab.github.io/__;!!DZ3fjg!4Q3ju2Smd6v_587Zx9HXVTP9mSzRGK8PT4DwmoyLylHQuMAf_kUmLHafqOWeM1cDZYzLStqXeef-ixXGpv9iLlb9RQU$ >