[gmx-users] suggestion for mk_angndx

David van der Spoel spoel at xray.bmc.uu.se
Thu Sep 2 08:55:06 CEST 2004

On Thu, 2004-09-02 at 07:37, Dallas Warren wrote:
> As a suggestions, may be change mk_angndx to be more like make_ndx
> where you can use the -n and -o switches.  I am following the
> dihedrals in a particular molecule type in my simulation, so to
> generate the appropriate dihedral index need to change the tpr file
> using tpbconv and select it to output the file for the molecule in
> interest then use mk_angndx.  No idea on how these things are working
> under the hood etc, just thought I might suggest it.
> Catch ya,

mk_angndx is not a very widely used tool. If you know the atom numbers
making up your dihedral it's just as easy to write a small script to do
it for you. Changing the tpr file should not be necessary...

If something then we maybe should merge the two programs, but I doubt
anyone will want to put time in this...
> Dr. Dallas Warren
> Research Fellow
> Department of Pharmaceutical Biology and Pharmacology
> Victorian College of Pharmacy, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9083
> --------------------------------------------------------------------------
> When the only tool you own is a hammer, every problem begins to
> resemble a nail.
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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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