[gmx-users] restraining Ca2+ ion
jayant james
jayant.james at gmail.com
Thu Jan 8 02:12:58 CET 2009
Hi!
Thanks for the reply. So would Gromos96 53a6 be available in the latest
version of GROMACS? I am currently using Gromacs version 3.3.3.
Thanks
JJ
On Wed, Jan 7, 2009 at 4:28 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>>
>>
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>>
>> -- ========================================
>>
>> 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
>>
>> ========================================
>>
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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>
>> <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 <http://vt.edu/> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
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>> http://www.gromacs.org/mailman/listinfo/gmx-users
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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>)
>>
>>
> --
> ========================================
>
> 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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