Recently, I am doing MD simulation of a copolymer. The monomer is a chemical had vinyl group, and uses the vinyl group to form polymer. My adviser asked me to do such an analysis to see how the branch distribute along the backbone. I though over that for about one month and I got a not bad solution to do that.
The principle of this analysis is finding the dihedral using the backbone and the other two atoms on the branch. The only problem is how to align all the backbone. Here, I use Schrödinger Maestro to do that. This app has an amazing function to adjust angle, bond, dihedral and maintain the original linked structure. The analysis can only deal with one frame. You need to extract the PDB file from trajectory file. Only keep the backbone and two atoms of each branch and strip other atoms. The detailed operation is below.
- Import the PDB file to Maestro
- use win+D to open the script editor
- Type adjustangle angle=180.0 2 3 4 in it and then adjustangle angle=180.0 3 4 6, adjustangle angle=180.0 4 6 7 …. adjustangle angle=180.0 93 94 96 (Assuming there are 96 residues in the polymer). Run the script.
- export the PDB file and then use CPPTRAJ to calculate the dihedral. Then you can plot how the branch distribute along with the backbone. I will release the GNUPLOT script in Part2.
Some key points for the analysis.
- When strip useless atoms in CPPTRAJ, remember to use PARMSTRIP to save a corresponding PRMTOP file for the dihedral calculation.
- The adjustangle should be done in order from the head atom 2 to the end atom 96. Otherwise, the distribution would be wrong.
- Maestro sometimes need to run same command twice to execute it (adjustangle angle=180.0 2 3 4, adjustangle angle=180.0 2 3 4). So you may need execute two same commands to adjust one angle. I usually use BASH to generate the Maestro script.