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
575 Stadium Mall Drive
West Lafayette, IN 47907-2091
(765)494-6564 office
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