Dear Gromacs Users,
I am confused about the definition of improper dihedral angle of Charmm
used in gromacs.
I used two molecle
1)M1: C6H5-NH2
2)MP1: C6H5-NH-C=O
|
CH3
After I submitted to the webserver of ParamChem, the output str files in
the attachment show that
*For M1*, IMPROPERS
NG2S3 HGP4 HGP4 CG2R61 -2.5000 0 0.00 ! -2.0 PYRIDINE
aminopyridine 11/10 kevo: sic! Compensates for in-plane force from
CG2R61 CG2R61 NG2S3 HGP4
*For MP1*, IMPROPERS
CG2O1 CG331 NG2S1 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK)
WILDCARD
For M1, with a NH2 group, ParamChem gives an improper dihedral *with N as a
central atom*.
However, for MP1, with a NH1 internal group, ParamChem does not give any
dihedrals *with N as a central atom*.
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