VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Fri Oct 13 2023 - 06:46:37 CDT

..and note the 0 for the improper from the error readout:

Info: PARAMETER file: CHARMM format!
Info: PARAMETERS
/Users/joelsubach/Desktop/PANX1_PROJECT/MODELLER_LOOP_MODEL/7dwbRCSB/7dwbRCSB_LoopModeling/BEST_MODEL/LIGANDS/Medusa_Docked_7dwb.BL04340001BEST_MODEL.pdb/GROMACS_Protein-Ligand_Complex/Step_.5/ffTK/ffTK_14C/1-sysPrep/par_14C.par
Info: PARAMETERS parZeroFile.par
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 21 BONDS
Info: 39 ANGLES
Info: 72 DIHEDRAL

*Info: 0 IMPROPER*Info: 0 CROSSTERM
Info: 15 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Warning: Ignored 116 angles with zero force constants.
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)

On Wed, Oct 11, 2023 at 4:05 PM Joel Subach <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://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf
> <https://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf>).*
>
> 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.)
>
> 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--0000000000009bf0c10607979c5b--