VMD-L Mailing List

From: francesco quilli (quilli.1855253_at_studenti.uniroma1.it)
Date: Mon Mar 11 2024 - 10:12:52 CDT

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