<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On May 3, 2010, at 6:27 PM, 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; ">They are on the inside of the structure. I don't think it is caused by a water molecule, because I ran editconf and genbox again and got the same result. (I have assumed that water molecules are added to the structure in a random fashion in areas not already occupied by other atoms)<br></div></span></blockquote>genbox is not necessarily able to place water molecules in small confined spaces </div><div>in a protein. You should check the pdb structure and see if there is not a water molecule</div><div>in that "space". Note that this was only a idea ... not necessarily your problem.</div><div>a better probe of the distance between the two residue side chain would be to use</div><div>the C of the COO group and the N of the NH3 group. You might observe reorientation </div><div>the the "satellite atoms" (O and H) while the center of the group is actually keeping </div><div>a reasonable distance.</div><div>Basically all goes in checking what kind of deformation you observe during your</div><div>minimization, a single distance is not necessarily meaningful. </div><div><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; ">If you like I can send you the structures in PDB form.<span class="Apple-converted-space"> </span><br></div></span></blockquote>Not necessary<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>> From:<span class="Apple-converted-space"> </span><a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a><br>> To:<span class="Apple-converted-space"> </span><a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>;<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> Subject: Re: [gmx-users] Unneccessary bonding<br>> Date: Mon, 3 May 2010 18:18:31 +0200<br>> CC:<span class="Apple-converted-space"> </span><br>><span class="Apple-converted-space"> </span><br>><span class="Apple-converted-space"> </span><br>> On May 3, 2010, at 6:12 PM, Justin A. Lemkul wrote:<br>><span class="Apple-converted-space"> </span><br>> ><br>> ><br>> > abdullah ahmed wrote:<br>> >> Dear Mr. Periole,<br>> >> The atoms that are getting close are oxygen from a GLU residue and<span class="Apple-converted-space"> </span><br>> >> hydrogen from a LYS residue.<br>> ><br>> > I don't see anything wrong with a 1.4-A distance between these<span class="Apple-converted-space"> </span><br>> > atoms. Why do you suspect a problem (besides the non-existent bond)?<br>> Agreed! This is fine ... the question is why they go from 3.5 to<span class="Apple-converted-space"> </span><br>> 1.4 ... are they<br>> embedded in the protein interior? At the surface of the protein ....<br>> may be a missing water molecule in between them?<br>> ><br>> > -Justin<br>> ><br>> >> Abdullah<br>> >> ------------------------------------------------------------------------<br>> >> From:<span class="Apple-converted-space"> </span><a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a><br>> >> To:<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> >> Subject: Re: [gmx-users] Unneccessary bonding<br>> >> Date: Mon, 3 May 2010 18:00:43 +0200<br>> >> On May 3, 2010, at 5:52 PM, abdullah ahmed wrote:<br>> >> Thank you very much for your reply, I agree it is probably a<span class="Apple-converted-space"> </span><br>> >> visualization of the effect, and that there<br>> >> is no bond. However, the distance between the two atoms<br>> >> participating in this "phantom bond" is 1.4 A°. Isn't that too<br>> >> close? Shouldn't it be considered a clash? 1.4 is short for<span class="Apple-converted-space"> </span><br>> >> sure! an H-bond goes down to 1.0 ... and charged ions make<span class="Apple-converted-space"> </span><br>> >> (depending on their size) bonds with water oxygen around 2.0 ... If<span class="Apple-converted-space"> </span><br>> >> you have two opposite charges in front of each other that might<span class="Apple-converted-space"> </span><br>> >> well be happening! What kind of atoms are the ones getting<span class="Apple-converted-space"> </span><br>> >> close? Abdullah<span class="Apple-converted-space"> </span><br>> >> ------------------------------------------------------------------------<br>> >> From: <a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a> <<a href="mailto:x.periole@rug.nl">mailto:x.periole@rug.nl</a>><br>> >> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <<a href="mailto:gmx-users@gromacs.org">mailto:gmx-users@gromacs.org</a>><br>> >> Subject: Re: [gmx-users] Unneccessary bonding<br>> >> Date: Mon, 3 May 2010 17:36:29 +0200<br>> >> On May 3, 2010, at 5:16 PM, abdullah ahmed wrote:<br>> >> Hello, I am a new user to GROMACS and so this<span class="Apple-converted-space"> </span><br>> >> question maybe somewhat<br>> >> naive. My objective is to run a few steps of<span class="Apple-converted-space"> </span><br>> >> minimization on a PDB<br>> >> structure and then obtain the energy value. To do so I ran the<br>> >> procedure suggested in the tutorial called "speptide" using<span class="Apple-converted-space"> </span><br>> >> the<br>> >> .mdp file provided in this procedure. The<span class="Apple-converted-space"> </span><br>> >> structure I am using has two oppositely charged residues<br>> >> facing each other. The initial distance(3.2 A°) is such that<br>> >> ionic interactions should occur between them, thereby<span class="Apple-converted-space"> </span><br>> >> creating a<br>> >> low coloumb energy score after minimization/molecular dynamics<br>> >> (check by looking at the log-file). However, a covalent bond<span class="Apple-converted-space"> </span><br>> >> is<br>> >> being created between them instead. This should not be<span class="Apple-converted-space"> </span><br>> >> happening. What do you mean a covalent bond is being created!<span class="Apple-converted-space"> </span><br>> >> This is basically<br>> >> not possible! Would that just be a visualization effect?<span class="Apple-converted-space"> </span><br>> >> This could result from<br>> >> the fact that the two atoms<br>> >> get really close to each other and thereby your visualization<br>> >> program thinks it is a covalent<br>> >> bond.<br>> >> Does anyone have any ideas on what may be happening and how I<br>> >> can fix it? If this information is not sufficient,<span class="Apple-converted-space"> </span><br>> >> please let me know, and<br>> >> thank you in advance.<br>> >> Abdullah Ahmed<span class="Apple-converted-space"> </span><br>> >> ------------------------------------------------------------------------<br>> >> Hotmail: Free, trusted and rich email service. Get it now.<br>> >> <<a href="https://signup.live.com/signup.aspx?id=60969">https://signup.live.com/signup.aspx?id=60969</a>> --<span class="Apple-converted-space"> </span><br>> >> gmx-users mailing list<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> >> <<a href="mailto:gmx-users@gromacs.org">mailto:gmx-users@gromacs.org</a>><br>> >><span class="Apple-converted-space"> </span><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> >> Please search the archive<br>> >> 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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Get Windows Live Hotmail Free.<span class="Apple-converted-space"> </span><br>> >> Sign<br>> >> up now. <<a href="https://signup.live.com/signup.aspx?id=60969">https://signup.live.com/signup.aspx?id=60969</a>> --<span class="Apple-converted-space"> </span><br>> >> gmx-users mailing list<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> >> <<a href="mailto:gmx-users@gromacs.org">mailto:gmx-users@gromacs.org</a>><br>> >><span class="Apple-converted-space"> </span><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<br>> >> posting!<br>> >> Please don't post (un)subscribe requests to the list. Use<span class="Apple-converted-space"> </span><br>> >> the www interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>> >> <<a href="mailto:gmx-users-request@gromacs.org">mailto:gmx-users-request@gromacs.org</a>>.<br>> >> Can't post? Read<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>> >> ------------------------------------------------------------------------<br>> >> Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign<span class="Apple-converted-space"> </span><br>> >> up now. <<a href="https://signup.live.com/signup.aspx?id=60969">https://signup.live.com/signup.aspx?id=60969</a>><br>> ><br>> > --<span class="Apple-converted-space"> </span><br>> > ========================================<br>> ><br>> > Justin A. 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