I have been trying to get the CG representation of a basic octane molecule. The pdb file is as follows:
ATOM 1 C1 BUT 1 2.142 1.395 -8.932 1.00 0.00ATOM 2 C2 BUT 1 3.631 1.416 -8.537 1.00 0.00ATOM 3 C3 BUT 1 4.203 -0.012 -8.612 1.00 0.00ATOM 4 C4 BUT 1 5.691 0.009 -8.218 1.00 0.00ATOM 5 1H1 BUT 1 1.604 0.760 -8.260 1.00 0.00ATOM 6 2H1 BUT 1 1.745 2.388 -8.880 1.00 0.00ATOM 7 3H1 BUT 1 2.043 1.024 -9.930 1.00 0.00ATOM 8 1H2 BUT 1 4.169 2.051 -9.210 1.00 0.00ATOM 9 2H2 BUT 1 3.731 1.788 -7.539 1.00 0.00ATOM 10 1H3 BUT 1 3.665 -0.647 -7.940 1.00 0.00ATOM 11 2H3 BUT 1 4.104 -0.384 -9.610 1.00 0.00ATOM 12 1H4 BUT 1 5.793 0.388 -7.201 1.00 0.00ATOM 13 2H4 BUT 1 6.240 0.656 -8.903 1.00 0.00ATOM 14 C1 MET 1 6.263 -1.418 -8.293 1.00 0.00ATOM 15 1H1 MET 1 6.162 -1.797 -9.309 1.00 0.00ATOM 16 2H1 MET 1 5.715 -2.065 -7.608 1.00 0.00ATOM 17 C1 MET 1 7.750 -1.397 -7.899 1.00 0.00ATOM 18 1H1 MET 1 7.852 -1.018 -6.882 1.00 0.00ATOM 19 2H1 MET 1 8.299 -0.750 -8.583 1.00 0.00ATOM 20 C1 MET 1 8.321 -2.824 -7.973 1.00 0.00ATOM 21 1H1 MET 1 8.221 -3.203 -8.990 1.00 0.00ATOM 22 2H1 MET 1 7.774 -3.471 -7.288 1.00 0.00ATOM 23 C1 MET 1 9.809 -2.803 -7.579 1.00 0.00ATOM 24 1H1 MET 1 10.214 -3.813 -7.632 1.00 0.00ATOM 25 2H1 MET 1 10.358 -2.156 -8.264 1.00 0.00ATOM 26 3H1 MET 1 9.911 -2.424 -6.562 1.00 0.00TER 27 MET 1 END I cannot understand how to run martinize.py once I have downloaded the whole repo from the source: https://github.com/cgmartini/martinize.py/tree/master . Do I run it as a shell script, if yes what is the command I should use to run MARTINI to merely get the CG .pdb representation of an AA .pdb