Dear Haddock Team,
Let’s say I have to staple a peptide. It requires unnatural amino acids and linker groups which are not present in Haddock force field. However, all atom force field parameters (CHARMM), which are used for MD simulations, is available.
In such situation, how do I translate the all atom molecular dynamics force field to haddock force field, and how trust-able are these translations?
This can be done, however it is not a trivial task and only relevant if the unnatural aminoacid is part of the interface. You need to manually create parameters, topologies and the links. You can only say how trustable this conversion is with proper benchmark.
However there might be a simpler solution, if the staple itself is not part of the interface you can instead define unambiguous restraints to emulate the same behaviour.