[gmx-users] restraining Ca2+ ion

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 8 01:28:33 CET 2009



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>> 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>>> 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/> | (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>)
> 
> 
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> 
>     -- 
>     ========================================
> 
>     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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