[gmx-users] PDB code

Nick Johans johans.nick93 at gmail.com
Wed Aug 29 17:20:45 CEST 2018


I'm a beginner in GROMACS and MD. I used pdb2gmx for having topology file
of PDB ID: 3e7y (lnsuline). It has 4 chains A,B,C,D after pdb2gmx. When you
google it, it is mentioned that insuline has 2 chains named A,B. So why
it's pdb code has 4 chains? Are they couple of each other? If yes and i
should remove C,D chains, is there any tool to remove them standardly
;)(not manually)?

How about Zn, Cl atoms there? Should i remove all nonbonded atoms when
starting simulation?

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