[gmx-users] About NME group construction

[David van der Spoel]

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

>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?

Have you run pdb2gmx and grompp? Have you checked warnings?


>
>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
>> > >
>> > >__________________________________________________________
>> > >_______________________________________________
>> > >gmx-users mailing list
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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
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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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++