[gmx-users] Segmentation fault - pdb2gmx specbond.dat
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?
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users