VMD-L Mailing List

From: Ernesto Aleksei Delgado Hurtado (ERDELGADO_at_UDEC.CL)
Date: Mon Mar 11 2024 - 17:21:46 CDT

Hi francesco

I can tell by the shape of your PES scans that you are trying to fit your parameters using the whole molecule.

The recommended approach is by dividing your molecules into smaller pieces that contain your functional groups of interest, fitting your parameters on those molecules and then copying the parameters to use on your whole molecule.

Regards,

Ernesto Delgado

El 11/3/24 a las 12:12, francesco quilli escribió:

Hi all,

I am currently working on resolving a dihedral belonging to a dioxa
azaspiro group. I have generated the QM target data, but I am encountering
difficulties in fitting the dihedral to the target.
I utilized the CGenFF program to identify entities with high penalties that
require further validation/optimization. Based on the output of CGenFF:

dihedral {CG321 CG321 CG3C50 OG3C51} K=3.4000 Periodicity 1 Phase shift=
180° Penalty=53;

I initiated a ±90° scan with a 15° step size. I attempted various
combinations (i.e., periodicities, phase shift angles, and optimization
algorithms as you can see in CG321_CG321_CG3C50_OG3C51.pdf), but I am
unable to reduce the RMSE beyond 1.769. Additionally, in the target data, I
observe a first minimum that is not reached in any of these profiles (PES
profile are shown in CG321_CG321_CG3C50_OG3C51.pdf), despite trying
different combinations, as mentioned above, I also attempted a ±90° scan
with a lower step size (10°), but the results are very similar.

I find myself stuck in this situation. Could anyone provide advice or tips
on this issue? Should I consider lowering the step size even further? I
would greatly appreciate any guidance.

PS: I'm using VMD 1.9.4 and ORCA 5.0.4.

Best,
Francesco