[gmx-users] -inter command
zaved at tezu.ernet.in
zaved at tezu.ernet.in
Fri Jan 19 14:34:02 CET 2018
> Message: 3
> Date: Thu, 18 Jan 2018 07:39:39 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] -inter command
> Message-ID: <0281054c-c062-90c3-2243-ef0f5f3ed6c2 at vt.edu>
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> On 1/18/18 7:02 AM, zaved at tezu.ernet.in wrote:
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>>> 1. Re: -inter command (Jo?o Henriques)
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>>> Date: Tue, 16 Jan 2018 08:30:10 +0100
>>> From: Jo?o Henriques <joao.m.a.henriques at gmail.com>
>>> To: gmx-users at gromacs.org
>>> Subject: Re: [gmx-users] -inter command
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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?
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
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.
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