[gmx-users] About g_dih analyze

[David]

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.

> 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++