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

Justin Lemkul jalemkul at vt.edu
Wed Aug 29 20:16:26 CEST 2018

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.


> 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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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