Re: [gmx-users] [BULK][EXT] Re: PDB code

2018-08-29 Thread Justin Lemkul
On 8/29/18 2:34 PM, Nick Johans wrote: Thank you dear justin. I'll read the paper. But practically it is mentioned that (for simulation) it has 51 residues which exactly equal to A,B chain. And i hope you answer the question about protonating " Residues B23-B30 were removed from insulin

Re: [gmx-users] [BULK][EXT] Re: PDB code

2018-08-29 Thread Nick Johans
Thank you dear justin. I'll read the paper. But practically it is mentioned that (for simulation) it has 51 residues which exactly equal to A,B chain. And i hope you answer the question about protonating " Residues B23-B30 were removed from insulin 43 residues. The C-terminal carboxyl groups

Re: [gmx-users] [BULK][EXT] Re: PDB code

2018-08-29 Thread Justin Lemkul
On 8/29/18 2:13 PM, Nick Johans wrote: Thank you so much Iris. want to simulate a protwin interaction with nanotube. The question is the pdb file structure. As i have not simulate protein before and i know that insulin has 2 chains the question is that why in pdbcode(3e7y) insulin has 4

Re: [gmx-users] [BULK][EXT] Re: PDB code

2018-08-29 Thread Nick Johans
Thank you so much Iris. want to simulate a protwin interaction with nanotube. The question is the pdb file structure. As i have not simulate protein before and i know that insulin has 2 chains the question is that why in pdbcode(3e7y) insulin has 4 chain? On Wed, 29 Aug 2018, 22:00 Smith, Iris,

Re: [gmx-users] [BULK][EXT] Re: PDB code

2018-08-29 Thread Smith, Iris
Hi Nick, I think the big question is what are you trying to simulate – what is your goal? It is critical that you now your protein (e.g. how was it crystalized, any missing atoms, missing residues, hetero atoms, ligands). I think prior to building your system you should first understand your