[gmx-users] restraining Ca2+ ion

[Justin A. Lemkul]

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>> 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
> 
> 
>         ------------------------------------------------------------------------
> 
> 
> 
>         _______________________________________________
>         gmx-users mailing list    gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>         http://www.gromacs.org/mailman/listinfo/gmx-users
>         Please search the archive at http://www.gromacs.org/search
>         before posting!
>         Please don't post (un)subscribe requests to the list. Use the
>         www interface or send it to gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>.
>         Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
>     -- 
>     ========================================
> 
>     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
> 
>     ========================================
> 
>     _______________________________________________
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://www.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
> 
> -- 
> Jayasundar Jayant James
> 
> www.chick.com/reading/tracts/0096/0096_01.asp 
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>)
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

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

========================================