[gmx-users] cdist and pdb2gmx -alldih

David spoel at xray.bmc.uu.se
Wed Apr 28 20:30:02 CEST 2004

On Wed, 2004-04-28 at 20:15, Ruben Martinez Buey wrote:
> Hi all,
> In the reference manual you can read for cdist:
> "The program uses proper dihedrals to give a distance too, as minimum
> respectively maximum the cis and trans configurations are taken. It is
> therefore beneficial to use the -alldih option
> of pdb2gmx to generate a topology with all dihedrals in there".
> But I cannot see the -alldih option in pdb2gmx... Is it on by defect?
It's gone! (it's in the force field definition files, e.g. OPLS gives
you all dihedrals).

Actually you should consider trying the concoord program from Bert de
Groot, since it has been tested better and has been updated recently.
The GROMACS version has never really worked well...

> Thanks in advance for your kind attention,
> Cheers,
> Ruben
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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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