[gmx-users] About NME group construction

[ygao at phase1.unl.edu]

Sorry, I made a mistake. I add the [NME] into  ffG43a1.rtp
But I encounter some problems when optimizing this structure, the peptide
is broken into two parts: other residues and NME. How to solve it?

Yi

On Tue, 15 Feb 2005 ygao at phase1.unl.edu wrote:

> 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)
> > >       1-402-310-4155 (M)
> > >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
> > spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
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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
>
> __________________________________________________________
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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

__________________________________________________________