Hello AMBER Users,
I am working with systems which have nonstandard C-terminal amino acid
residues (such as norleucine, tert-leucine, norvaline, etc.). When using
Parmchk2 to check for missing parameters from parm10.dat, only this was
given:
IMPROPER
CX-O2-C -O2 10.5 180.0 2.0 Using general improper
torsional angle X-O2-C-O2, penalty score= 3.0
I was able to recreate this with standard C-terminal amino acid residues
(by loading the ff14SB force field into LEaP, saving a .mol2 file
corresponding to CLEU and CVAL, then running Parmchk2 on those .mol2
files). The same dihedral parameter and comment were reported in the
resulting .frcmod files.
Can anyone with more experience tell me how significant of a penalty score
this is, and if it is worth trying to fix using paramfit or mdgx? I mention
it because this parameter is also missing for standard amino acid residues,
and not just the nonstandards that I built myself.
All the best,
-NDB
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Received on Tue Mar 08 2022 - 22:00:02 PST
