Dear Gmx Users,<br><br>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:<br>
<br>10<br>POS SOD 4 POS SOD 4 0.36 POS POS<br>POS SOD 4 NEG CLA 4 0.36 POS NEG<br>POS SOD 4 POL N 4 0.36 POS POL<br>POS SOD 4 NON C 4 0.36 POS NON<br>
NEG CLA 4 NEG CLA 4 0.36 NEG NEG<br>NEG CLA 4 POL N 4 0.36 NEG POL<br>NEG CLA 4 NON C 4 0.36 NEG NON<br>POL N 4 POL N 4 0.36 POL POL<br>
POL N 4 NON C 4 0.36 POL NON<br>NON C 4 NON C 4 0.36 NON NON<br><br>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:<br>
<br>.....<br>Linking POL-397 N-397 and NEG-398 CLA-398...<br>Linking NEG-398 CLA-398 and NON-399 C-399...<br>Linking NON-399 C-399 and POL-400 N-400...<br>Segmentation fault (core dumped)<br><br>The Gromacs is installed on the cluster - version 4.5.5. I tried also on 4.5.4. and the same happens.<br>
<br>Could you please advise?<br><br>Steven<br>