On 1/20/18 2:26 AM, za...@tezu.ernet.in wrote:
Message: 1
Date: Tue, 16 Jan 2018 08:30:10 +0100
From: Jo?o Henriques <joao.m.a.henriq...@gmail.com>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] -inter command
Message-ID:
<CAHv45qOCV7fOu8heK0q1w_=gdzmevrcxz35ct8xxzfwwngu...@mail.gmail.com>
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Thank you so much Joao Sir for your kind response.
1. I have predicted the pka values for my protein using H++ server.
2. Based on the pka values, I have set the protonation states of the
charged residues using -inter command for pH 9.
3.I have run my simulation at pH 9 (keeping charge of +8e) using
gromacs
5.1.4 and gromos54a7 ff.
After performing 100ns simulation, I didn't observed any change
compared
to control system.
Can you provide any advice on it?
In what ways do the "pH 9" and "control" simulations differ? What do
you
define as "control" in this instance, default protonation by pdb2gmx?
If
that's the case, unless you have some very noncanonical pKa values,
there's nothing that's really expected to be different between these
two
pH values, except perhaps the N-terminus itself.
What are you trying to compare or calculate? Perhaps 100 ns is
insufficient to observe whatever it is you're after. How have you
quantified that there is no difference/change between these systems?
-Justin
Thank you so much Justin.
1. Yes you are correct. control here means default protonation state and
in this case the system charge of +8e is neutralized. I didn't have any
noncanonical pka values (at ph9). Checked with both H++ server and
Propka.
For ph 9, I have kept the charge of +8e.
2. Our experimental data suggests that at higher pH (9), the protein
initiates unfolding.
3. I have taken the final structure (at 100ns) of both systems and
superimposed it. I got a RMSD of 1.030 angstrom and no major structural
change was observed.
4. We can consider to extend the simulation to visualize any change, if
above things are correct.
There won't be one. Since the topologies are identical, you're running
the same simulation twice, and concluding that there are no major
variations between the two. You don't actually have any simulation that
you can claim is representing anything other than "pH 7," though pH
isn't really a thing in fixed-charge/fixed-topology MD. This is a
limitation of modeling something with fixed protonation states; it
doesn't necessarily reflect reality. A constant pH method might show
some results, but AFAIK this is not possible in GROMACS (though some
people do have custom code in old versions that might work). You may
want to consider a different program like AMBER or CHARMM that can do
these types of simulations.
-Justin
Thank You so much Justin.
Can you provide the name and any link for older gromacs version?
People who have done this use their own custom versions of whatever they
choose. Look in the literature; this feature is not officially supported
by GROMACS.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
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.biochem.vt.edu/people/faculty/JustinLemkul.html
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