On 8/15/24 8:37 AM, Pedro Guillem via modeller_usage wrote: > I'm using Modeller to mutate only. I was wondering how hard it would be > to mutate any position into a non-standard residue. I have my residues > in Amber format (frcmod+off), and I read that I must create the > definitions in CHARMM (RST) format, so modeller understands its > topology+charges,etc.
If I were in your position, I would just run a short constrained simulation in Amber instead, since you already have the files in the right format and Amber will likely do a better job with the non-standard residue anyway. Modeller is primarily designed for comparative modeling, and so relies on template information; in cases like mutation where you don't have this information, it's not going to do as good a job.
> I see that ParmED (for example) can import the Amber files and generate > RST files from them, but I didn't fully understand how many files I must > modify in modeller, or whether I should use the BLK option, but it is > not very well documented how to do so.
A BLK or '.' residue just copies the residue's coordinates from the template and then treats it as a rigid body. That's probably not going to be useful here since a) you don't have a template and b) you presumably want to relax the conformation of the mutated residue.
Ben Webb, Modeller Caretaker