Hello everyone,
I have generated random coordinates of 25 bead polyethylene molecule using rotational isomeric state theory. While trying to visualize in VMD or Material Studio software package, I'm getting a very unusual cage like structure coming up on the screen and the beads are not connected in successive manner. One bead is connected to multiple atoms it seems. In the remark section, its showing 25 atoms and 109 bonds and sometimes 63 bonds.
I have checked the distance between each atom of the PE molecule and it is equal to the C-C Bond length of 1.53 Angstroms.
I'm attaching one of the PDB file I'm trying to visualize having coordinates of 25 bead PE Chain
What might be the possible reason for such a problem ? Please help
I visualized this file in PyMol and it looks OK, as a polymer should look like.
Your PDB file is, however, inconsistent with the PDB format: there should be one more whitespace between the last coordinate (z) and the "1.00" column in each row starting with ATOM. Some visualizers are very strict when reading the PDBs and may not display it properly.
Also, some visualizers do not read the CONECT part of the PDB at all and try guessing connectivities based on the distances, which sometimes may lead to strange results. VMD definitely does not read the CONECT records. This is not a thing to worry, just a visualization problem.
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