[gmx-users] Possible Bug????

[Berk Hess]

Hi,

The eigenvector file is only stored in .trr format for coding convenience.
It was never intended to be used with trjconv etc.
But if you want to use it that way you indeed have to use editconf
to make a structure file with only the atoms you used in the analysis,
as you did.

I don't know why you want to write the eigenvectors to pdb.
They will not give you meaningful structures.

g_anaeig has several options to visualize eigenvectors.

Berk.

> Date: Thu, 24 Jul 2008 15:49:56 -0400
> From: mldaniel at pharmacy.purdue.edu
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Possible Bug????
> 
> Users,
> 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:
> Command:
>       trjconv -f eigenvec.trr -s prot_md.gro -o test.pdb
> Output:
> 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???
> Thanks!
> -- 
> 
> Matthew L. Danielson
> 
> Graduate Student of Medicinal Chemistry & Molecular Pharmacology
> College of Pharmacy, Nursing, and Health Sciences
> Purdue University
> MCMP RHPH 516
> 575 Stadium Mall Drive
> West Lafayette, IN 47907-2091
> 
> (765)494-6564 office
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