[gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue 93

[Bakary N'tji Diallo]

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>:

> Send gromacs.org_gmx-users mailing list submissions to
>         gromacs.org_gmx-users at maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
>         gromacs.org_gmx-users-request at maillist.sys.kth.se
>
> You can reach the person managing the list at
>         gromacs.org_gmx-users-owner at maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> 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
> Message-ID:
>         <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.
> gmail.com>
> >>>>> 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
>
>
>
>
> * * * D I S C L A I M E R * * *
> This e-mail may contain privileged information and is intended solely for
> the individual named. If you are not the named addressee you should not
> disseminate, distribute or copy this e-mail. Please notify the sender
> immediately by e-mail if you have received this e-mail in error and destroy
> it from your system. Though considerable effort has been made to deliver
> error free e-mail messages but it can not be guaranteed to be secure or
> error-free as information could be intercepted, corrupted, lost, destroyed,
> delayed, or may contain viruses. The recipient must verify the integrity of
> this e-mail message.
>
>
> ------------------------------
>
> 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
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 165, Issue 93
> ******************************************************
>



-- 

*Bakary*