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 > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > 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 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
