[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
>
>
>
> ------------------------------------------------------------------------
>
>
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto: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>
> <mailto: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/> <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>
> <mailto: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>
> <mailto: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>
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>)
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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>)
>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list