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, <jalem...@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, <smit...@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-boun...@maillist.sys.kth.se> on behalf of
Nick Johans <johans.nic...@gmail.com>
Reply-To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
Date: Wednesday, August 29, 2018 at 11:36 AM
To: "gmx-us...@gromacs.org" <gmx-us...@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.nic...@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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Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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