[4] Implement frame based backmapping

[jan-stevens]

In this pull request, the frame-based backmapping protocol's first version will be implemented. The most basic idea is that users provide internal reference frames for each residue, which will be applied to the (user-provided) residue templates.

[cesar-lopez-bau]

Is the backmapping implemented yet?

[jan-stevens]

Is the backmapping implemented yet?

Hi Cesar! We're still wrapping up the final implementation of this protocol, but most of the functionality is implemented. Can you tell us which molecule you're working with? Perhaps we can assist you in using this branch?

[cesar-lopez-bau]

Hi Jan;

Thanks for the response. I’m implementing my own polyply library based on charmm36 for carbohydrates. Now I want to have a way to transform back and for from martini. I kinda solve the problem using the regular backward tool, but it is cumbersome having to also work in the mapping files for backward when could be done only in polyply, specially when I’m working in 20 different polymers. Could you tell me how to work with it, let’s say for the dextran case?

thanks

Cesar

César López Bautista Staff scientist Los Alamos National Laboratory

On Dec 14, 2023, at 1:33 AM, Jan Stevens @.***> wrote:

Is the backmapping implemented yet?

Hi Cesar! We're still wrapping up the final implementation of this protocol, but most of the functionality is implemented. Can you tell us which molecule you're working with? Perhaps we can assist you in using this branch?

— Reply to this email directly, view it on GitHub https://github.com/marrink-lab/polyply_1.0/pull/341#issuecomment-1855403148, or unsubscribe https://github.com/notifications/unsubscribe-auth/A7NTPBESOOHU2YAEEZFX3JLYJK2VZAVCNFSM6AAAAAA3QZGNIWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJVGQYDGMJUHA. You are receiving this because you commented.

[fgrunewald]

@cesar-lopez-bau that sounds exciting! Are you going to share your CHARMM implementation at some point?

To address your problem I've created a discussion thread (https://github.com/marrink-lab/polyply_1.0/discussions/353) with an example on how to backmap dextran to charmm using the current functionality without the need for a frame-based backmapping. The generated coordinates look reasonable, even though I think the frame-based method can be a bit more precise. @jan-stevens will show you the frame-based version based on that example.

In case you are going to test the regular backmapping strategy, let us know if there are any problems you might encounter.

[cesar-lopez-bau]

It works like a charm, I’ll finishing implementing other libraries and let you know so you can added into the repository

thanks

Cesar

César López Bautista Staff scientist Los Alamos National Laboratory

On Dec 20, 2023, at 3:12 AM, Dr. Fabian Grunewald @.***> wrote:

@cesar-lopez-bau https://github.com/cesar-lopez-bau that sounds exciting! Are you going to share your CHARMM implementation at some point?

To address your problem I've created a discussion thread (#353 https://github.com/marrink-lab/polyply_1.0/discussions/353) with an example on how to backmap dextran to charmm using the current functionality without the need for a frame-based backmapping. The generated coordinates look reasonable, even though I think the frame-based method can be a bit more precise. @jan-stevens https://github.com/jan-stevens will show you the frame-based version based on that example.

In case you are going to test the regular backmapping strategy, let us know if there are any problems you might encounter.

— Reply to this email directly, view it on GitHub https://github.com/marrink-lab/polyply_1.0/pull/341#issuecomment-1864204948, or unsubscribe https://github.com/notifications/unsubscribe-auth/A7NTPBDJFQNPOLP734TEOFDYKK22XAVCNFSM6AAAAAA3QZGNIWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRUGIYDIOJUHA. You are receiving this because you were mentioned.