[gmx-users] About NME group construction

[David van der Spoel]

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

>Thanks for your suggestion. I add below line into *.hdp
There is no such file, but that probaby is a typo.

Add it to aminoacids.dat as well.

>
>[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
>
>__________________________________________________________
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>

-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++