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

[Justin Lemkul]

On 3/3/14, 12:27 AM, Tom 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*.
>

It shouldn't.  The CHARMM force field uses few improper dihedrals in general, 
and there are none around N in acetamides.  See examples in model compounds like 
NMA, DMA, etc in the CHARMM force fields.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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