amber14sb_OL15.ff correction in Dihedrals

Third party tools and files
1

Dear collegues! Right now I revealed that there is a mistake in amber14sb_OL15.ff.
File ffbonded.itp should be modified in lines 801-804. Instead of

801 CT CV CC NA 4 180.00 4.60240 2
802 CT CW CC NA 4 180.00 4.60240 2
803 NB CW CC CT 4 180.00 4.60240 2
804 CT CW CC NB 4 180.00 4.60240 2

Should be written:

801 CT CV CC NA 4 180.00 4.60240 2
802 NA CV CC CT 4 180.00 4.60240 2
803 NB CW CC CT 4 180.00 4.60240 2
804 CT CW CC NB 4 180.00 4.60240 2

This mistake is cause of Error “No default Per. Imp. Dih. types” in case if Histidine with ND hydrogen [HID residue] appear in your protein.

2

Could you please provide more background on why this is the case? I ran into the same issue with a missing improper dihedral for HISD which was corrected by including the “802 NA CV CC CT 4 180.00 4.60240 2” line in the ffbonded.itp files. Notably, this did not match the order of the atoms in which the improper dihedral was not found, in my simulation (CT C CV NA). Yet it still worked. Will this be fixed in the future?

3

could you provide more details? thanks a lot