g_anaeig: Segmentation fault upon reading in eigenvec.trr
I have gromacs3.3.1 on Ubuntu 6.06 - installed using synaptic package manager.
I have a receptor (552 residues) bound to a peptide (6 to 9 residues) and I want to investigate the dynamics of just the receptor without the peptide.
I used make_ndx to make an index file with only CA of the receptor.
Then used g_covar to generate the eigenvectors of the covar. matrix, where the input traj (a series of PDB files concat. together with ENDMDL as a seperator) is that of the receptor bound to the peptide. Everything worked fine (or at least there's no error messages.)
Next, Using g_anaeig -v eigenvec.trr -eig eigenvalue.xvg -proj -first 1 -last 10 gives a segmentation fault. (I've tried just g_anaeig -v eigenvec.trr and the same error appears).
#3 Updated by ZT Yew over 12 years ago
Created an attachment (id=239)
Frames of PDB
I've attached a PDB with frames from a trajectory. I did the following as well as the steps I stated in my first post:
1. make_ndx: index file with CA atoms and residues 1-294 only using complex.pdb
2. g_covar: g_covar -f complex_frames.pdb -s Complex.pdb -n index.ndx -o eigenval.out -v eigenvec.trr
3. g_anaeig: g_anaeig -f complex_frames.pdb -s Complex.pdb -n index.ndx -v eigenvec.trr -proj project1_5.out -first 1 -last 5
4. tried g_anaeig -v eigenvec.trr as well
Error is 'Segmentation fault' at the g_anaeig step
I'll attach complex.pdb later
#7 Updated by ZT Yew over 12 years ago
I installed gromacs3.3.1 on ubuntu 7.04 and tried to repeat with the files I attached and it works.
So its either a problem with a previous installation on ubuntu 6.06 or something to do with the fact (though unlikely) that I tried it with 2000 frames and the file I attached has only 200?
I will attempt to do the analysis with 2000 frames on ubuntu 7.04
Thanks for your help!
#8 Updated by David van der Spoel over 12 years ago
Most likely a compilation issue, but it could also be a rare bug that only shows up on some machines. I have tested it in my Mac and on a Debian box (which previously showed some problems), and I couldn't reproduce it. Obviously we cannot support all possible OS version. But I will try in the lab to install a box with this.