[gmx-users] xtc files

[YOLANDA SMALL]

Thanks David,
That works!

On Tue, 14 Mar 2006 08:49:43 +0100, David van der Spoel wrote:

> YOLANDA SMALL wrote:
> > Hi All,
> > 
> > How do I convert xtc files exported for a subset of atoms in my system to
pdb
> > files?
> > 
> > When I run trjconv, I get the following error message:
> > 
> > Fatal error: Index[0] 3611 is larger than the number of atoms in the
trajectory
> > file (3152)
> > 
> > In my mdp file I specify the option 'xtc_grps' to export a subset of solvent
and
> > protein atoms to an xtc file. This subset of atoms is defined in my index
file
> > and contains 3152 atoms. Then I discard the .trr files to save space.  It
looks
> > like the atom index gets renumbered from 1 in the new .xtc file so that the
new
> > atom indeces no longer correspond to the atoms in the original coordinate
file.
> >  How do I recover the coordinates with matching atom names from the .xtc
file?
> > 
> Sorry I misread your question.
> You make a pdb file from your original tpr using the same index group 
> you used for the xtc-grps, then you use this pdb file as reference for 
> trjconv on the xtc to pdb conversion.
> > Thanks,
> > Yolanda
> > 
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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://folding.bmc.uu.se
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