VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Thu Mar 14 2024 - 03:51:15 CDT

There may be other correlated dihedrals which also require simultaneous
fitting, even if they have low penalty scores, this usually fixes the
problem for me.

*Daniel Fellner BSc(Hons)*
PhD Candidate | Research Assistant
School of Chemical Sciences
University of Auckland
Ph +64211605326

On Thu, 14 Mar 2024 at 21:06, francesco quilli <
quilli.1855253_at_studenti.uniroma1.it> wrote:

> 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
>>
>>
>>
>>
>>