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:
10 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? Steven
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