Hi Sunny, Justin is right in saying that the hydrogen bonds will be absent in the coarse grained file. For MARTINI, you would need to get the secondary structure information from the original, un-CG .pdb file (in your case, your 1K4C clean pdb file). When doing the topology, it will become clear that the .ssd file that is required will be that obtained from your original pdb file. That is how the MARTINI force field works. I hope this helps!
Best, --Johnny -- ------------------------------------------------- Johnny Lam ISPE Berkeley Chapter External Vice President Department of Bioengineering College of Engineering University of California, Berkeley Tel: (408) 655- 6829 Email: [email protected]
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