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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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