[gmx-users] About g_dih analyze

[ygao at phase1.unl.edu]

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?

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

__________________________________________________________