[gmx-users] PDB code

Nick Johans johans.nick93 at gmail.com
Wed Aug 29 17:36:27 CEST 2018

Sorry, i have just removed C,D chains by pymol and then started
simulating(without adding any terminal or H,...)... but after grompp, the
system had charges and were not integer. Is it because of i didn't add
terminals? I use AMBER99SB forcefield and as you know it doesn't work with
-ter but i have read paper which is said( that's my reference paper);
" Residues B23-B30 were
removed from insulin 43 residues. The C-terminal carboxyl groups and all
the charged residues were set to be
protonated to simulate the protein structures under acidic conditions.
Parameterized force field parameters for
protonated C-terminal carboxyl groups were used (Hong et al., 2012)."
What does it mean  "protonated" ? How they add H when they have used AMBER
 Would you please help me?

Best regards
On Wed, 29 Aug 2018, 19:50 Nick Johans, <johans.nick93 at gmail.com> wrote:

> Hi,
> 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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