On 4/4/24 2:30 PM, Qizan Chen wrote: > 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.
Yes, you would need to parse the restraints file (https://salilab.org/modeller/10.5/manual/node503.html), replace some subset of the restraints with your custom restraints, and then rerun Modeller with that custom restraint file. As I said, it would be a lot of work!
> 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.
Right, max_molpdf saves computer time by quickly discarding very bad models with large scores. But since max_molpdf is a fixed value (10^7) but pdf scales roughly with the square of the number of atoms in your system, for very large systems it might throw out valid models. So you can increase it in this case: https://salilab.org/modeller/10.5/manual/node52.html
Ben Webb, Modeller Caretaker