[gmx-users] About NME group construction
ygao at phase1.unl.edu
ygao at phase1.unl.edu
Tue Feb 15 22:00:55 CET 2005
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.
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
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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
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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
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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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> _______________________________________________
> gmx-users mailing list
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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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