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

Wed Aug 29 20:34:53 CEST 2018

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 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)."
I didn't protonate the molecule, so when i used grompp, my system had not
integer charges, is it because of i ignore the polar groups and didn't
protonate carboxyl groups?

Best
On Wed, 29 Aug 2018, 22:46 Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> 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 chain?
> >
>
> You need to read the paper associated with that crystal structure as
> well as header information in the PDB file as to why this is. A crystal
> complex is not necessarily the same as a functional complex.
>
> -Justin
>
> > 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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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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