VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Sat Oct 14 2023 - 12:15:04 CDT

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