[modeller_usage] Re: Perodic boundary condition?

[Qizan Chen <qz.chen AT tamu.edu>]

It seems difficult to implement PBC with custom restraints for me, because
I can't even don't know which default constraints need to be modified.

About the crashes, previously I ran on Ubuntu 18.04, it failed for
segmentation fault. Today I updated my Linux to 22.04, and now it won't
crash, but a max_molpdf issue arises.

Anyway, thank you so much for your reply!

Best regards!
Qizan Chen

On Wed, Apr 3, 2024 at 5:09 PM Modeller Caretaker <modeller-care@ucsf.edu>
wrote:

> On 4/3/24 12: 56 PM, Qizan Chen via modeller_usage wrote: > Can the
> Modeller take periodic boundary conditions into account > during modeling?
> No, Modeller has no built-in support for periodic boundary conditions. You
> can add custom restraints
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> On 4/3/24 12:56 PM, Qizan Chen via modeller_usage wrote:
> > Can the Modeller take periodic boundary conditions into account
> > during modeling?
>
> No, Modeller has no built-in support for periodic boundary conditions.
>
> You can add custom restraints to the scoring function (see, e.g.https://urldefense.com/v3/__https://salilab.org/modeller/10.5/manual/node480.html__;!!KwNVnqRv!FEsVBNeNXXDaWyxUiaKFAWJcZ9qoPeyXU0A37txR3gELwNKm2ZgFAbqH1_EnMFItfijS3Y0yH5xKo5lSaKdnQDR7Sg$) so in principle
> you could replace the existing restraints with PBC-aware versions, e.g.
> rather than calculating the distance between A and B, return the
> distance between A and the nearest image of B. However, this would be a
> significant undertaking.
>
> > I noticed that symmetry constraints can be added
>
> They can, but Modeller's symmetry restraints would likely not be very
> efficient here, since they don't remove any degrees of freedom.
>
> > but my original system is already large, and adding additional images
> > causes crashes.
>
> Modeller should not crash with any size system, unless you run out of
> physical memory, so I'm curious to know what your problem is here.
>
> 	Ben Webb, Modeller Caretaker
> -- modeller-care@ucsf.edu             https://urldefense.com/v3/__https://salilab.org/modeller/__;!!KwNVnqRv!FEsVBNeNXXDaWyxUiaKFAWJcZ9qoPeyXU0A37txR3gELwNKm2ZgFAbqH1_EnMFItfijS3Y0yH5xKo5lSaKepbghP-g$
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>

It seems difficult to implement PBC with custom restraints for me, because I can't even don't know which default constraints need to be modified.

About the crashes, previously I ran on Ubuntu 18.04, it failed for segmentation fault. Today I updated my Linux to 22.04, and now it won't crash, but a max_molpdf issue arises.

Anyway, thank you so much for your reply!

Best regards!

Qizan Chen

On Wed, Apr 3, 2024 at 5:09â?¯PM Modeller Caretaker <modeller-care@ucsf.edu> wrote:

On 4/3/24 12:â??56 PM, Qizan Chen via modeller_usage wrote: > Can the Modeller take periodic boundary conditions into account > during modeling? No, Modeller has no built-in support for periodic boundary conditions. You can add custom restraints

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On 4/3/24 12:56 PM, Qizan Chen via modeller_usage wrote:
> Can the Modeller take periodic boundary conditions into account
> during modeling?

No, Modeller has no built-in support for periodic boundary conditions.

You can add custom restraints to the scoring function (see, e.g.
https://urldefense.com/v3/__https://salilab.org/modeller/10.5/manual/node480.html__;!!KwNVnqRv!FEsVBNeNXXDaWyxUiaKFAWJcZ9qoPeyXU0A37txR3gELwNKm2ZgFAbqH1_EnMFItfijS3Y0yH5xKo5lSaKdnQDR7Sg$) so in principle
you could replace the existing restraints with PBC-aware versions, e.g.
rather than calculating the distance between A and B, return the
distance between A and the nearest image of B. However, this would be a
significant undertaking.

> I noticed that symmetry constraints can be added

They can, but Modeller's symmetry restraints would likely not be very
efficient here, since they don't remove any degrees of freedom.

> but my original system is already large, and adding additional images
> causes crashes.

Modeller should not crash with any size system, unless you run out of
physical memory, so I'm curious to know what your problem is here.

	Ben Webb, Modeller Caretaker
-- 
modeller-care@ucsf.edu             https://urldefense.com/v3/__https://salilab.org/modeller/__;!!KwNVnqRv!FEsVBNeNXXDaWyxUiaKFAWJcZ9qoPeyXU0A37txR3gELwNKm2ZgFAbqH1_EnMFItfijS3Y0yH5xKo5lSaKepbghP-g$
Modeller mail list: https://urldefense.com/v3/__https://salilab.org/mailman/listinfo/modeller_usage__;!!KwNVnqRv!FEsVBNeNXXDaWyxUiaKFAWJcZ9qoPeyXU0A37txR3gELwNKm2ZgFAbqH1_EnMFItfijS3Y0yH5xKo5lSaKc-UBdTNA$