[gmx-users] About g_dih analyze

ygao at phase1.unl.edu ygao at phase1.unl.edu
Tue Feb 22 22:18:54 CET 2005 

I cannot solve it yet. Would you kindly tell me whether there is any other
software to get the information of the dihedral angles from .trr file?

Yi


On Tue, 22 Feb 2005, David wrote:

> On Tue, 2005-02-22 at 14:29 -0600, ygao at phase1.unl.edu wrote:
> > On Tue, 22 Feb 2005, David wrote:
> >
> > > On Tue, 2005-02-22 at 10:45 -0600, ygao at phase1.unl.edu wrote:
> > > > I use the ffgmx2 (all atom) force field. But when I generate the .tpr
> > > > file, there are some errors:
> > > >
> > > > WARNING 1 [file "ala.top", line 96]:
> > > >   No default Angle types, using zeroes
> > > > WARNING 2 [file "ala.top", line 98]:
> > > >   No default Angle types, using zeroes
> > > > WARNING 3 [file "ala.top", line 99]:
> > > >   No default Angle types, using zeroes
> > > > WARNING 4 [file "ala.top", line 120]:
> > > >   No default Angle types, using zeroes
> > > > WARNING 5 [file "ala.top", line 121]:
> > > >   No default Angle types, using zeroes
> > > > WARNING 6 [file "ala.top", line 122]:
> > > >   No default Angle types, using zeroes
> > > > WARNING 7 [file "ala.top", line 129]:
> > > >   No default Proper Dih. types, using zeroes
> > > > WARNING 8 [file "ala.top", line 134]:
> > > >   No default Proper Dih. types, using zeroes
> > > > Cleaning up temporary file grompplsoWJY
> > > > Fatal error: Atomtype 'K' not found!
> > > >
> > > > However, I never use K atom in my system. What's the problem and how to
> > > > solve?
> > > >
> > > use opls.
> >
> > I'm sorry that I don't understand it. I want to analysis the dihedral
> > angles of peptides with OPLS/AA+SPC model, but g_dih told me
> >
> > Reading file ala-spc-10ns.tpr, VERSION 3.2.1 (single precision)
> > Found 1 phi-psi combinations
> > Fatal error: Dihedral around 6,8 not found in topology
> >
> > You told me earlier that I'd better to use the ffgmx2 (all atom) force
> > field to generate .tpr file to analyze this traj. Now I got error
> > messages:
> >
> > No default Angle types, using zeroes
> > WARNING 2 [file "ala.top", line 98]:
> >  No default Angle types, using zeroes
> > WARNING 3 [file "ala.top", line 99]:
> > No default Angle types, using zeroes
> > WARNING 4 [file "ala.top", line 120]:
> >  No default Angle types, using zeroes
> > WARNING 5 [file "ala.top", line 121]:
> >  No default Angle types, using zeroes
> > WARNING 6 [file "ala.top", line 122]:
> > No default Angle types, using zeroes
> > WARNING 7 [file "ala.top", line 129]:
> > No default Proper Dih. types, using zeroes
> > WARNING 8 [file "ala.top", line 134]:
> > No default Proper Dih. types, using zeroes
> > Cleaning up temporary file grompplsoWJY
> > Fatal error: Atomtype 'K' not found!
> >
> > So I don't know what I should do now. Would you kindly tell me how to do
> > next? Thanks!
> Sorry, forgot about that. OK, just use this topology for the analysis.
> If grompp doesn't like it just increase the max number of warnings.
> >
> > Yi
> >
> > >
> > > > Yi
> > > >
> > > > On Sat, 19 Feb 2005, David van der Spoel wrote:
> > > >
> > > > > On Fri, 18 Feb 2005 ygao at phase1.unl.edu wrote:
> > > > >
> > > > > >Hi,gromacs-user,
> > > > > >
> > > > > >I'm using the OPLS/AA+SPC model to simulate a small peptide. After
> > > > > >simulation, I want to analyze the dihedral angles of this peptide. But
> > > > > >when I use the command line below:
> > > > > >
> > > > > >g_dih -s ala-spc-10ns.tpr -f ala-spc-10ns.trr
> > > > > >
> > > > > >There're some error message:
> > > > > >
> > > > > >Reading file ala-spc-10ns.tpr, VERSION 3.2.1 (single precision)
> > > > > >Found 1 phi-psi combinations
> > > > > >Fatal error: Dihedral around 6,8 not found in topology
> > > > > >
> > > > > >I read the geometry with VMD, and found no problem.
> > > > > >
> > > > > >I'd like to know how to solve it?
> > > > > The problem is that some GROMOS specific information is hardcoded in the
> > > > > program. A possible solution would be to make a new tpr file using the
> > > > > ffgmx2 (all atom) force field *JUST FOR THIS ANALYSIS*.
> > > > >
> > > > >  >
> > > > > >Yi
> > > > > >
> > > > > >__________________________________________________________
> > > > > >
> > > > > >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
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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
> > 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
> 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

__________________________________________________________

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