[gmx-users] restraining Ca2+ ion
Justin A. Lemkul
jalemkul at vt.edu
Thu Jan 8 02:35:04 CET 2009
jayant james wrote:
> Hi!
> Thanks for the reply. So would Gromos96 53a6 be available in the latest
> version of GROMACS? I am currently using Gromacs version 3.3.3.
pdb2gmx -h will give you a list of all the force fields distributed with Gromacs.
-Justin
> Thanks
> JJ
>
> On Wed, Jan 7, 2009 at 4:28 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> jayant james wrote:
>
> Hi!
>
> Thanks for the reply.
> I am using the option 0 of pdb2gmx which corresponds to GROMOS96
> 43a1 force field. But earlier today I was linked to a thesis
> which used GROMACS force field so I am still wondering if it
> would be right for me to go to the *.top file and change the
> charges to amino acids for simulations in GROMOS96 force field
> found in GROMACS package.
>
>
> I tend to opt for the most recent revision of a modern force field,
> something like Gromos96 53a6, unless there is a specific basis for a
> choice like 43a1 (i.e., consistency with previous work, parameters
> that have been specifically developed for use with that parameter
> set, etc.) Otherwise, blindly choosing a force field with no basis
> for the choice is not a good idea.
>
> If you are considering making ad hoc changes to your .top to force a
> certain behavior, I think you are asking for trouble, especially if
> it comes to peer review. Force fields aren't designed to be
> tinkered with according to the whim of a user. If you are willing
> to expend a great deal of effort in developing new parameters to
> accurately replicate real-life behavior, then by all means do so.
> Otherwise, I would be very suspicious of results that come from
> untested modifications.
>
> -Justin
>
> Thanks
> JJ
>
>
> On Wed, Jan 7, 2009 at 3:07 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> jayant james wrote:
>
> Hi!
> In the protein of my interest I find that oxygen atoms of
> Thr,
> Tyr and Ser are close to the bound Ca2+. So is there any
> information on charge modifications that need to be made
> for the
> specified amino acids in the gromacs force field, such
> that the
> Ca2+ would stay and not stray!
>
>
> I should hope you're not using the "Gromacs force field"
> (ffgmx), it
> has long been deprecated. You are better off with a more modern
> Gromos96 parameter set.
>
> I think the best procedure would first to refer to the
> citation you
> were provided earlier today, then proceed with a further
> literature
> search. Has anyone simulated a similar protein with any success?
> You may be in for some parameterization if you find the existing
> parameters inadequate. Beware, such work is very difficult.
>
> -Justin
>
> Thanks
> Jayant James
>
>
>
> On Wed, Jan 7, 2009 at 10:36 AM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>> wrote:
>
>
>
> jayant james wrote:
>
> Hi!
> Thanks for your suggestions. In my protein there
> are two
> phosphorylated serines (-vely charged) adjacent to
> each
> other on
> chain A and these serines start to move towards
> the Ca2+
> ion in
> chain B. It is only after a while of them being
> close to each
> other that the Ca2+ starts popping off. Also to
> modify the
> charges of the residues adjoining the Ca2+ ion,
> what file
> should
> I be looking for to make these changes? would it
> be the
> topology
> file?
>
>
> Well, that behavior may not be entirely unexpected.
> Two adjacent
> phosphates would likely repel each other, making it
> difficult to
> bind ions at that location. Is there some basis to
> suggest that
> Ca2+ should even bind there?
>
> Yes, charges are in your topology. If you generated your
> .top with
> pdb2gmx, then obviously there are entries in the
> appropriate .rtp
> file that can be modified to generate future
> topologies with the
> same charges.
>
>
> As per your suggestions I would be going with the
> PME so
> should
> the mdp file modified to incorporate the
> parameters below be
> sufficient?!!
>
> Well, assuming those are the appropriate cutoff's for
> your force
> field, and the rest of your .mdp file is satisfactory
> (and you
> actually specify PME), then it is probably reasonable
> enough.
>
> -Justin
>
> ns_type = grid
> rlist = 1.0
> rcoulomb = 1.0
> rvdw = 1.4
> vdwtype = cut-off
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nx = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> disre = simple
> disre_weighting = equal
> Thanks
> Jayant James
>
>
>
> ------------------------------------------------------------------------
>
>
>
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> -- ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/>
> <http://vt.edu/> | (540)
>
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> -- Jayasundar Jayant James
>
> www.chick.com/reading/tracts/0096/0096_01.asp
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>)
>
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>
>
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> -- ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/> | (540)
> 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> Jayasundar Jayant James
>
> www.chick.com/reading/tracts/0096/0096_01.asp
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>)
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> Jayasundar Jayant James
>
> www.chick.com/reading/tracts/0096/0096_01.asp
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>)
>
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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