[gmx-users] Re: trjconv modification

[David]

On Sun, 2002-12-22 at 14:49, Graham Smith wrote:
> 
> Hi - 
> 
> I've been finding that, when dealing with several simulations of
> different mutants of a protein, or a complexed and uncomplexed form,
> the current indexing facilities of trjconv make it very difficult to
> fit the different trajectories to the same structure file as you might
> wish (e.g. fit on C-alphas, output all protein atoms).  Therefore I've
> modified trjconv so that it can take two index groups, -n and -ns. -ns
> then selects from the structure file and -n selects from the
> trajectory and controls the output.  I've put it on the contributions
> page. 

If you have just a few conformations you can use g_confrms, it already
takes two index files.
> 
> This is designed for use with -fit only, and output should be to an
> xtc or trj (the res/atom fields in a pdb or gro will be wrong). The
> output is often slightly different to the standard version but the
> difference is always small (<= 0.005 A). 
> 
> Cheers 
> 
> Graham 
> 
> ########################################################################
> 
> Dr. Graham R. Smith,
> Biomolecular Modelling Laboratory,
> Cancer Research UK,
> 44 Lincoln's Inn Fields,
> London WC2A 3PX,
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 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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