<div>Hi!</div>
<div>Thanks for the reply.</div>
<div>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.</div>
<div>Thanks</div>
<div>JJ<br><br></div>
<div class="gmail_quote">On Wed, Jan 7, 2009 at 3:07 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="Ih2E3d"><br><br>jayant james wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi!<br>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!<br>
</blockquote><br></div>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.<br><br>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.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Thanks<br>Jayant James
<div>
<div></div>
<div class="Wj3C7c"><br><br><br> On Wed, Jan 7, 2009 at 10:36 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br><br> jayant james wrote:<br><br> Hi!<br> Thanks for your suggestions. In my protein there are two<br> phosphorylated serines (-vely charged) adjacent to each other on<br> chain A and these serines start to move towards the Ca2+ ion in<br>
chain B. It is only after a while of them being close to each<br> other that the Ca2+ starts popping off. Also to modify the<br> charges of the residues adjoining the Ca2+ ion, what file should<br> I be looking for to make these changes? would it be the topology<br>
file?<br><br><br> Well, that behavior may not be entirely unexpected. Two adjacent<br> phosphates would likely repel each other, making it difficult to<br> bind ions at that location. Is there some basis to suggest that<br>
Ca2+ should even bind there?<br><br> Yes, charges are in your topology. If you generated your .top with<br> pdb2gmx, then obviously there are entries in the appropriate .rtp<br> file that can be modified to generate future topologies with the<br>
same charges.<br><br><br> As per your suggestions I would be going with the PME so should<br> the mdp file modified to incorporate the parameters below be<br> sufficient?!!<br> <br><br> Well, assuming those are the appropriate cutoff's for your force<br>
field, and the rest of your .mdp file is satisfactory (and you<br> actually specify PME), then it is probably reasonable enough.<br><br> -Justin<br><br> ns_type = grid<br> rlist = 1.0<br>
rcoulomb = 1.0<br> rvdw = 1.4<br> vdwtype = cut-off<br> fourierspacing = 0.12<br> fourier_nx = 0<br> fourier_ny = 0<br> fourier_nx = 0<br>
pme_order = 4<br> ewald_rtol = 1e-5<br> optimize_fft = yes<br> disre = simple<br> disre_weighting = equal<br> Thanks<br> Jayant James<br><br><br> ------------------------------------------------------------------------<br>
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<div class="Wj3C7c"><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Graduate Research Assistant<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br>
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