[gmx-users] About NME group construction
David van der Spoel
spoel at xray.bmc.uu.se
Tue Feb 15 22:11:53 CET 2005
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
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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
>> >>
>> >> __________________________________________________________
>> >> _______________________________________________
>> >> 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
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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
>> 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
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