[gmx-users] restraining Ca2+ ion
jayant james
jayant.james at gmail.com
Thu Jan 8 01:12:11 CET 2009
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.
Thanks
JJ
On Wed, Jan 7, 2009 at 3:07 PM, Justin A. Lemkul <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>> 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/> | (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>)
>>
>>
>> ------------------------------------------------------------------------
>>
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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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