[gmx-users] restraining Ca2+ ion

[jayant james]

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!
Thanks
Jayant James



On Wed, Jan 7, 2009 at 10:36 AM, Justin A. Lemkul <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 | (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)
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