[gmx-users] About NME group construction

ygao at phase1.unl.edu ygao at phase1.unl.edu
Tue Feb 15 22:13:10 CET 2005 

I use this command line to generate the ala.ndx:

/home/zeng/chgy/para-gromacs/x86_64-unknown-linux-gnu/bin/pdb2gmx -f a.pdb
-o ala.gro -p ala.top -ter -n ala.ndx

And the ala.ndx file is below:

[ prot_sort ]
   1    2    3    4    5    6    7    8    9   10   11   12

Do you know what does this mean?

Yi


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

> On Tue, 15 Feb 2005 ygao at phase1.unl.edu wrote:
>
> >Now the optimization is no problem. But when I run grompp to try to do md
> >process, there are some error messages:
> >
> >Walking down the molecule graph to make shake-blocks
> >initialising group options...
> >processing index file...
> >Fatal error: Group Protein not found in indexfile.
> it's probably what is says: you have no group Protein in your file ala.ndx
>
> >Maybe you have non-default goups in your mdp file, while not using the
> >'-n' option of grompp.
> >In that case use the '-n' option.
> >
> >However, my command line is:
> >
> >/home/zeng/chgy/para-gromacs/x86_64-unknown-linux-gnu/bin/grompp -f
> >dyn-1ns.mdp -c ala-min.gro -p ala.top -o ala-spc-10ns.tpr -t ala-min.trr
> >-n ala.ndx
> >
> >Do you know how to solve it? By the way, I've added the NME into the
> >aminoacids.dat.
> >
> >Yi
> >
> >
> >
> >On Tue, 15 Feb 2005, David van der Spoel wrote:
> >
> >> 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
> >> >> > >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
> >> >> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> >> >
> >> >> > _______________________________________________
> >> >> > 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.
> >> >> >
> >> >>
> >> >> __________________________________________________________
> >> >>
> >> >> 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.
> >> >>
> >> >
> >> >__________________________________________________________
> >> >
> >> >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
> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>
> >> _______________________________________________
> >> 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.
> >>
> >
> >__________________________________________________________
> >
> >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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> _______________________________________________
> 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.
>

__________________________________________________________

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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