[gmx-users] Segmentation fault - pdb2gmx specbond.dat

Steven Neumann s.neumann08 at gmail.com
Wed Jun 6 15:06:27 CEST 2012

Dear Gmx Users,

I created a plane surface made of 4 different atoms (400 atoms togehter).
Each atom correspond to different residue - I added them to the
aminoacids.rtp file. They are placed in different positions with LJ radius
of 1.7A and they their center is 3.6 A away from each other (0.2A between
atom LJsurfaces). I want to create bonds between all of them so I added
specbonds.dat to my working directory:

POS    SOD    4    POS    SOD    4    0.36    POS    POS
POS    SOD    4    NEG    CLA    4    0.36    POS    NEG
POS    SOD    4    POL    N    4    0.36    POS    POL
POS    SOD    4    NON    C    4    0.36    POS    NON
NEG    CLA    4    NEG    CLA    4    0.36    NEG    NEG
NEG    CLA    4    POL    N    4    0.36    NEG    POL
NEG    CLA    4    NON    C    4    0.36    NEG    NON
POL    N    4    POL    N    4    0.36    POL    POL
POL    N    4    NON    C    4    0.36    POL    NON
NON    C    4    NON    C    4    0.36    NON    NON

So that all of them can create bonds with each of them being within the
distance of 3.6A. When I process to pdb2gmx where the matrix is created and
bonds are being linked when the last residues are linked:

Linking POL-397 N-397 and NEG-398 CLA-398...
Linking NEG-398 CLA-398 and NON-399 C-399...
Linking NON-399 C-399 and POL-400 N-400...
Segmentation fault (core dumped)

The Gromacs is installed on the cluster - version 4.5.5. I tried also on
4.5.4. and the same happens.

Could you please advise?

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