[gmx-users] About NME group construction

[ygao at phase1.unl.edu]

Thanks for your suggestion. I add below line into *.hdp

[NME]
 [ atoms ]
    N     N    -0.28000     0
    H     H     0.28000     0
   CA   CH3     0.00000     1
 [ bonds ]
    N     H    gb_2
    N    CA    gb_20
 [ angles ]
;  ai    aj    ak   gromos type
   -C     N     H     ga_31
    H     N    CA     ga_17
   -C     N    CA     ga_30
 [ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_4

But when I optimize the structure, this group is separated with other
residues. Would you kindly tell me what's the problem? Thanks.

Yi


On Tue, 15 Feb 2005, David van der Spoel wrote:

> On Tue, 15 Feb 2005 ygao at phase1.unl.edu wrote:
>
> >
> >Hi,
> >
> >I want to construct -NHME group in GROMACS. Would you kindly tell me how
> >to construct it, or use any existing parameter to replace it, such as
> >ffG43a1 force field?
> >
> Check what's available already. Otherwise just mutate a Gly residue in the
> rtp and hdb files.
>
> >Yi Gao
> >
> >__________________________________________________________
> >
> >Department of Chemistry
> >University of Nebraska -- Lincoln
> >Lincoln, NE, USA 68508
> >
> >Phone: 1-402-472-9982 (O)
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> >Email: ygao at phase1.unl.edu
> >
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>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
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__________________________________________________________

Department of Chemistry
University of Nebraska -- Lincoln
Lincoln, NE, USA 68508

Phone: 1-402-472-9982 (O)
       1-402-310-4155 (M)
Email: ygao at phase1.unl.edu

__________________________________________________________