<div>Hi!</div>
<div>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! </div>
<div>Thanks</div>
<div>Jayant James</div>
<div><br><br> </div>
<div class="gmail_quote">On Wed, Jan 7, 2009 at 10:36 AM, 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>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? <br>
</blockquote><br></div>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?<br>
<br>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.
<div class="Ih2E3d"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">As per your suggestions I would be going with the PME so should the mdp file modified to incorporate the parameters below be sufficient?!!<br>
<br></blockquote><br></div>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.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="Ih2E3d">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></div>------------------------------------------------------------------------
<div class="Ih2E3d"><br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
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<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><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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<div class="Wj3C7c"><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
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<br><a href="http://www.chick.com/reading/tracts/0096/0096_01.asp">www.chick.com/reading/tracts/0096/0096_01.asp</a>) <br><br>