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

Smith, Iris smithi4 at ccf.org
Wed Aug 29 19:29:41 CEST 2018

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 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)."
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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