[gmx-users] About g_dih analyze

David van der Spoel spoel at xray.bmc.uu.se
Sat Feb 19 02:04:02 CET 2005

On Fri, 18 Feb 2005 ygao at phase1.unl.edu wrote:

>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*.

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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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