[gmx-users] Possible Bug????

Matthew Danielson mldaniel at pharmacy.purdue.edu
Thu Jul 24 21:49:56 CEST 2008

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[267] 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???

Matthew L. Danielson

Graduate Student of Medicinal Chemistry & Molecular Pharmacology
College of Pharmacy, Nursing, and Health Sciences
Purdue University
575 Stadium Mall Drive
West Lafayette, IN 47907-2091

(765)494-6564 office

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