Aim: ab-initio protein-modeling-docking for proteins containing non-standard amino acids .
I was able to parameterize the new amino acids for Amber ff, which developed along QM calculations for also K-Br atoms, i.e., at higher level than 6-31G* and DFT in place of HF. It worked: the MD simulation showed protein stability along 15 ns by using a NAMD-CUDA cluster.
Then, I collected info from Rosetta.3.3 forum, especially about mol2 file -> Rosetta parameters, such as in the thread initiated by einew on 02/28/2011 on "Rosetta applications".
Question: In Amber protocols, the mol2 file is not enough, it must be accompanied by a "frcmod" file for geometrical data. Is it any protocol about that? Once I hopefully succeed, I'll post the scheme.
thanks for advice