<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On May 11, 2010, at 11:37 AM, abdullah ahmed wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; ">Dear GROMACS users,<span class="Apple-converted-space"> </span><br><br>I have a protein structure with two oppositely charged residues facing each other. They are close enough for an electrostatic interaction to occur between them. However, this does not occur. After minimization they are in the exact same positions as before.<span class="Apple-converted-space"> </span><br></div></span></blockquote>So you have a new problem? Now you do not have the interaction anymore!?!??! </div><div>Last week you had it too close and wanted to avoid your residues to come that close!</div><div><br></div><div>Last week you also had several persons giving you advices about this issue and </div><div>everyone I believe agreed that this was certainly not the way to proceed to show </div><div>the effect or potential effect of a mutation. </div><div>More than a meaningless minimization a graphic illustration of the salt-bridge broken </div><div>by the mutation would probably be a better argument. </div><div><br></div><div>If you want a meaningful number you'll have to go for more sophisticated methods.</div><div><br></div><div>Note that the difference you see is 1000 kJ/mol, this is not small! </div><div><br></div><div>XAvier.<br><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; "><br>Is there some way to confirm that an electrostatic interaction is not being made in the structure with two charged residues facing each other? And if this is the case, do you have any idea as to why this is happening?<br><br>Perhaps the following information will prove helpful:<span class="Apple-converted-space"> </span><br><br><ul><li>I have another structure where there is only one charge (GLU) and one uncharged residue in the same positions as the charged residues in the previous structure. The coulomb energy values of the two structures after minimization do not show much difference (-3.9e+04 compared to -4.0e+4, where -4.0e+04 corresponds to the structure with two charges facing each other). Theoretically, this difference should be greater as the unsatisfied single charge is not as stable. To me the similar coloumb energies suggest that the electrostaic interactions are not being made in the structure with two opposite charges.</li></ul><br><ul><li>My .mdp file is as follows:</li></ul> ;<br> ; User spoel (236)<br> ; Wed Nov 3 17:12:44 1993<br> ; Input file<br> ;<br> cpp = /usr/bin/cpp<br> define = -DFLEXIBLE<span class="Apple-converted-space"> </span><br> constraints = none<br> integrator = steep<br> nsteps = 1000<br> ;<br> ; Energy minimizing stuff<br> ;<br> emtol = 2000<br> emstep = 0.01<br><br> nstcomm = 1<br> ns_type = grid<br> rlist = 1<br> rcoulomb = 1.0<br> rvdw = 1.0<br> Tcoupl = no<br> Pcoupl = no<br> gen_vel = no<br><br><br>Thank you in advance!<br>Abdullah <span class="Apple-converted-space"> </span><br><br> <br><br><hr>Hotmail: Powerful Free email with security by Microsoft.<span class="Apple-converted-space"> </span><a href="https://signup.live.com/signup.aspx?id=60969" target="_new">Get it now.</a><span class="Apple-converted-space"> </span>--<span class="Apple-converted-space"> </span><br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. 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