[gmx-users] Question about Improper Dihedral of Charmm in gmx & ParamChem

Tom dnaafm at gmail.com
Mon Mar 3 06:27:48 CET 2014

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
After I submitted to the webserver of ParamChem, the output str files in
the attachment show that


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

CG2O1 CG331 NG2S1 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK)

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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