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 <>
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$) so in principle
> you could replace the existing restraints with PBC-aware versions, e.g.
> rather than calculating the distance between A and B, return the
> distance between A and the nearest image of B. However, this would be a
> significant undertaking.
>
> > I noticed that symmetry constraints can be added
>
> They can, but Modeller's symmetry restraints would likely not be very
> efficient here, since they don't remove any degrees of freedom.
>
> > but my original system is already large, and adding additional images
> > causes crashes.
>
> Modeller should not crash with any size system, unless you run out of
> physical memory, so I'm curious to know what your problem is here.
>
> Ben Webb, Modeller Caretaker
> -- https://urldefense.com/v3/__https://salilab.org/modeller/__;!!KwNVnqRv!FEsVBNeNXXDaWyxUiaKFAWJcZ9qoPeyXU0A37txR3gELwNKm2ZgFAbqH1_EnMFItfijS3Y0yH5xKo5lSaKepbghP-g$
> Modeller mail list: https://urldefense.com/v3/__https://salilab.org/mailman/listinfo/modeller_usage__;!!KwNVnqRv!FEsVBNeNXXDaWyxUiaKFAWJcZ9qoPeyXU0A37txR3gELwNKm2ZgFAbqH1_EnMFItfijS3Y0yH5xKo5lSaKc-UBdTNA$
>
>
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 <">> 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