[gmx-users] Possible Bug????
mldaniel at pharmacy.purdue.edu
Thu Jul 24 22:13:00 CEST 2008
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.
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.
Matthew L. Danielson
Graduate Student of Medicinal Chemistry & Molecular Pharmacology
College of Pharmacy, Nursing, and Health Sciences
MCMP RHPH 516
575 Stadium Mall Drive
West Lafayette, IN 47907-2091
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