[gmx-users] Possible Bug????

[David van der Spoel]

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.
> -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.
>>
>>
>>
>>
> 


-- 
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