[modeller_usage] Re: Using frcmod+off non-standard residue in modeller.

[Modeller Caretaker <>]

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
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