[gmx-users] Possible Bug????
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jul 24 22:23:57 CEST 2008
Matthew Danielson wrote:
> Thanks for the reply, but i am a little unsure why the number of
> "atoms/coordinates" do not match. My eigenvec.trr has 1401 atoms (this
> was created using the same default index file to select the backbone)
> and it should match what is in my index file (or tpr).
> If i look at the index group listing (see below please) the backbone is
> listed with 1401 elements not the reported 1403 in the error message
> (see below), this is why i am confused.
but in your protein there are more than 1401 atoms, and hence backbone
atoms will have indices larger than 1401.
> Ill look into the g_anaeig program though, thanks for the suggestion.
> David van der Spoel wrote:
>> Matthew Danielson wrote:
>>> I am having a problem when trying to convert a .trr to a .pdb using
>>> trjconv. I think there could there be a bug in the program and the
>>> index group is getting confused. Here is exactly what i am doing:
>>> trjconv -f eigenvec.trr -s prot_md.gro -o test.pdb
>>> Will write pdb: Protein data bank file
>>> Select group for output
>>> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
>>> Group 0 ( System) has 68361 elements
>>> Group 1 ( Protein) has 7588 elements
>>> Group 2 ( Protein-H) has 3780 elements
>>> Group 3 ( C-alpha) has 467 elements
>>> Group 4 ( Backbone) has 1401 elements
>>> Group 5 ( MainChain) has 1867 elements
>>> Group 6 (MainChain+Cb) has 2307 elements
>>> Group 7 ( MainChain+H) has 2305 elements
>>> Group 8 ( SideChain) has 5283 elements
>>> Group 9 ( SideChain-H) has 1913 elements
>>> Group 10 ( Prot-Masses) has 7588 elements
>>> Group 11 ( Non-Protein) has 60773 elements
>>> Group 12 ( FLP) has 30 elements
>>> Group 13 ( SOL) has 60741 elements
>>> Group 14 ( Cl) has 2 elements
>>> Group 15 ( Other) has 60773 elements
>>> Select a group: 4
>>> Selected 4: 'Backbone'
>>> trn version: GMX_trn_file (single precision)
>>> Reading frame 0 time 0.000
>>> Back Off! I just backed up test.pdb to ./#test.pdb.1#
>>> Program trjconv, VERSION 3.3.2
>>> Source code file: gmx_trjconv.c, line: 994
>>> Fatal error:
>>> Index 1403 is larger than the number of atoms in the trajectory
>>> file (1401)
>>> I have been able to get around this problem (really only a work
>>> around this bug). Here is what i have done:
>>> editconf -f prot_md.gro -o eigenvec_base.gro -n index.ndx
>>> output only the Backbone atoms, and then run trjconv with the output
>>> from editconf as the template file (-s file). This then will
>>> translate the .trr file to a .pdb.
>>> Has anyone else seen this, or have any ideas???
>> This is the normal behavior. Your eigenvec was made based on backbone
>> and therefore has 1401 "coordinates", however in your index file (or
>> tpr) there are more atoms, and hence the index for backbone atoms is
>> larger than 1401.
>> Your workaround will create a gro/pdb file, but since the eigenvectors
>> are sorted this will not give you normal coordinates. You may want to
>> study the options built into the g_anaeig program.
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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