[gmx-users] Re: dssp output of CG structure of 1K4C

Johnny Lam johntus at berkeley.edu
Wed Aug 19 00:04:44 CEST 2009

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!


Johnny Lam
ISPE Berkeley Chapter External Vice President
Department of Bioengineering
College of Engineering
University of California, Berkeley
Tel: (408) 655- 6829
Email: johntus at berkeley.edu
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