Scoring

Is there perhaps a (python) script lying around somewhere in the src distribution to convert charmm parameter files (.prm) into mm_torsion_params.txt and mm_atom_properties.txt (in the database directory database\chemical\mm_atom_type_sets\fa_standard)?
I have added the MM parameters for R1A and now I naturally have a lot of missing types for the mm_* score terms. I’m thinking the easiest way to sort this out is just to regenerate the mm_torsion_params.txt and mm_atom_properties.txt from my working charmm parameter files?

Hi,
I used flexpepdock_score_only find the rmsca between 2 complexes. I also caculated the rmsca between the 2 complexes ((deltax^2+deltay^2+deltaz^2)^0.5) but the rmsCA score I got was different than the one I got using flexpepdock_score_only. Why is that happening?

Note - both complexes have the same sequence of aa.

Thanks!

Hello,

I'd like to decompose the energy in one body energy terms (for each residue) and pairwise energy terms for residue-residue interactions.
I tried to check if I could decompose these terms and sum them up to retrieve the score returned by the scoring function.
The problem is that I try 3 different ways of computing the energy, and I get 3 different numbers.
Could someone please tell me what's wrong ?

Here is my code:

Is it possible to approxmate the CHARMM energy (function) by the rosetta scoring function?

As a starting point I could work with fixed angles and bond lengths, so I guess setting the weghts for fa_atr, fa_rep and fa_elec to 1 and all the rest to zero is a good start. But is it possible to somehow load the CHARMM diheral parameters?

Thank you for your help,
Ajasja Ljubetič