VMD-L Mailing List

From: francesco quilli (quilli.1855253_at_studenti.uniroma1.it)
Date: Thu Mar 14 2024 - 02:55:24 CDT

 Thanks for the prompt responses,

The dioxa azaspiro group is already a fragment of a larger molecule; the
dihedral of interest is located at the center of this group, and it is
impossible to fragment it further.

I analyzed the rotation using the Torsion Explorer tool, and the generated
conformations do not seem to present steric clashes.

As recommended, I conducted tests with a smaller step size: Scan +-90° Step
size 5° and Scan +-90° Step size 3°. As can be observed from the PES scans
(PES profiles are shown in CG321_CG321_CG3C50_OG3C51.pdf), not much has
changed since the previous tests (Scan +-90° Step size 15° and Scan +-90°
Step size 10°), and the problem persists. I would appreciate your advice on
what I could try to improve these PES profiles.

Best regards,
Francesco

Il giorno mar 12 mar 2024 alle ore 03:43 Gumbart, JC <
gumbart_at_physics.gatech.edu> ha scritto:

> Indeed, it’s possible that steric clashes are interfering with the
> rotation, which creates those somewhat unusual PMFs. But at the very
> least, decreasing the step size is a good idea. The PMFs look rough.
>
> Best,
> JC
>
> On Mar 11, 2024, at 6:21 PM, Ernesto Aleksei Delgado Hurtado <
> ERDELGADO_at_UDEC.CL> wrote:
>
> 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
>
>
>
>
>