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

[Mark Abraham]

That is indeed strange, but perhaps best discussed with the authors of
ParamChem, after checking their documentation!

Mark
On Mar 3, 2014 6:32 AM, "Tom" <dnaafm at gmail.com> wrote:

> 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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