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

[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, <smithi4 at ccf.org> wrote:

> 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 goal
> and get a stronger foundation on MDS as well as the forcefiled you require
> to model your system, this will help you better understand the flags for
> each gmx command.
>
> I would start with first reading the gromacs manual and re-reading the
> reference paper associated with your PDB. Present your hypothesis and
> goal(s) to your colleagues – this will help you formulate a
> hypothesis-driven project.
>
> Iris
>
>
>
> [/Users/smithi4/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1833992660]
>
> Iris Nira Smith  |  Postdoctoral Fellow |  Genomic Medicine Institute
> Cleveland Clinic  |  9500 Euclid Ave. / NE5-255  |  Cleveland, OH 44195  |
> (216) 445-7885
>
>
>
>
> From: <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
> Nick Johans <johans.nick93 at gmail.com>
> Reply-To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Date: Wednesday, August 29, 2018 at 11:36 AM
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [BULK][EXT] Re: [gmx-users] PDB code
>
> 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)."
>
And how should protonate molecule in AMBER ff?

What does it mean "protonated" ? How they add H when they have used AMBER
> forcefield?
> 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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