[gmx-users] About g_dih analyze
ygao at phase1.unl.edu
ygao at phase1.unl.edu
Tue Feb 22 23:19:13 CET 2005
On Tue, 22 Feb 2005, David wrote:
> On Tue, 2005-02-22 at 15:18 -0600, ygao at phase1.unl.edu wrote:
> > 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?
> Yes, g_angle also does it, you have to define which ones you want
> manually then (in an index file).
Would you kindly tell me more explicitly? I did the steps afterwards:
(1) I modify the .ndx file as below:
[ System ]
1 2 ......
[ MainChain ]
5 7 9 15
7 9 15 17
(2) I used command line:
g_angle -s ala-spc-10ns.tpr -f ala-spc-10ns.trr -n ala-w.ndx -of
ala-dih-10ns.xvg
Now I get some error messages:
Group 0 ( System) has 6952 elements
Group 1 ( Protein) has 22 elements
Group 2 ( Protein-H) has 10 elements
Group 3 ( C-alpha) has 1 elements
Group 4 ( Backbone) has 5 elements
Group 5 ( MainChain) has 7 elements
Group 6 (MainChain+Cb) has 8 elements
Group 7 ( MainChain+H) has 9 elements
Group 8 ( SideChain) has 13 elements
Group 9 ( SideChain-H) has 3 elements
Group 10 ( Prot-Masses) has 22 elements
Group 11 ( Non-Protein) has 6930 elements
Group 12 ( SOL) has 6930 elements
Group 13 ( Other) has 6930 elements
Group 14 ( MainChain) has 8 elements
Select a group: 14
Selected 14: 'MainChain'
Fatal error: number of index elements not multiple of 3, these can not be
angle triplets
Do you know what's the problem? Thanks in advance!
Yi
> >
> > 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
> > > > > > > >
> > > > > > > >__________________________________________________________
> > > > > > > >_______________________________________________
> > > > > > > >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
> > > > > > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > > 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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> > > > > > 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
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> > > > > 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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