[gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue 93
Bakary N'tji Diallo
diallobakary4 at gmail.com
Sat Jan 20 21:46:23 CET 2018
Using the "grep" command in the force field
forlder (/usr/local/gromacs/share/gromacs/top/charmm27.ff$ , for example
"grep MG" or "grep Mg" can help.
2018-01-20 11:00 GMT+00:00 <
gromacs.org_gmx-users-request at maillist.sys.kth.se>:
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> Today's Topics:
> 1. -inter command (zaved at tezu.ernet.in)
> 2. interaction force between Mg and Oxygens of phosphate, in
> CHARM36 force field (Sajad Ahrari)
> Message: 1
> Date: Sat, 20 Jan 2018 12:56:03 +0530
> From: zaved at tezu.ernet.in
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] -inter command
> <66ef38054aecb55b37823b8a75aa529e.squirrel at webmail.tezu.ernet.in>
> Content-Type: text/plain;charset=utf-8
> >>>>> Message: 1
> >>>>> 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
> >>>>> Message-ID:
> >>>>> <CAHv45qOCV7fOu8heK0q1w_=GDZMEvRCXz35CT8xXzFWWNgUtiQ at mail.
> >>>>> Content-Type: text/plain; charset="UTF-8"
> >>>> 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?
> Thank You
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> Message: 2
> Date: Sat, 20 Jan 2018 07:42:55 +0000 (UTC)
> From: Sajad Ahrari <sajadahrari at yahoo.com>
> To: Discussion List for GROMACS Users
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] interaction force between Mg and Oxygens of
> phosphate, in CHARM36 force field
> Message-ID: <1389118376.1478181.1516434175184 at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
> Hello Dears,
> I am using CHARM-36.ff for my simulation. I have Mg ions and ATP as
> hetero-atoms in my system (the Mg-ATP complex). I am trying to know about
> the amount of interaction force between Mg ions and phosphates of ATP that
> is already set in this force field. Could you please help me know if I can
> find about these parameters in the force field files?
> Thank you
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> End of gromacs.org_gmx-users Digest, Vol 165, Issue 93
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