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

Wed Aug 29 20:39:42 CEST 2018

On 8/29/18 2:34 PM, Nick Johans wrote:
> 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?

No, the quoted passage means all amino acids were treated in their 
conjugate acid form (i.e. the dominant form at extremely low pH). This 
has nothing to do with a non-integer charge, simply that if you did not 
do the same thing, you're going to get protonation according to the 
dominant form at neutral pH. If you don't have an integer, you have a 
problem that pdb2gmx should have warned you about (long bonds => missing 
atoms, etc.)

-Justin

> 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
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
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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
http://www.thelemkullab.com

==================================================