[gmx-users] restraining Ca2+ ion
jayant.james at gmail.com
Wed Jan 7 22:55:01 CET 2009
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!
On Wed, Jan 7, 2009 at 10:36 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> jayant james wrote:
>> 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
> 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.
> 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
>> Jayant James
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> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
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Jayasundar Jayant James
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