[gmx-users] Possible Bug????

[Matthew Danielson]

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.
-M-

David van der Spoel wrote:
> Matthew Danielson wrote:
>> 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!
> 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
Purdue University
MCMP RHPH 516
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West Lafayette, IN 47907-2091

(765)494-6564 office