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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><br>If you like I can send you the structures in PDB form. <br><br>> From: x.periole@rug.nl<br>> To: jalemkul@vt.edu; gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Unneccessary bonding<br>> Date: Mon, 3 May 2010 18:18:31 +0200<br>> CC: <br>> <br>> <br>> On May 3, 2010, at 6:12 PM, Justin A. Lemkul wrote:<br>> <br>> ><br>> ><br>> > abdullah ahmed wrote:<br>> >> Dear Mr. Periole,<br>> >> The atoms that are getting close are oxygen from a GLU residue and <br>> >> hydrogen from a LYS residue.<br>> ><br>> > I don't see anything wrong with a 1.4-A distance between these <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 <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: x.periole@rug.nl<br>> >> To: gmx-users@gromacs.org<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 <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 <br>> >> sure! an H-bond goes down to 1.0 ... and charged ions make <br>> >> (depending on their size) bonds with water oxygen around 2.0 ... If <br>> >> you have two opposite charges in front of each other that might <br>> >> well be happening! What kind of atoms are the ones getting <br>> >> close? Abdullah <br>> >> ------------------------------------------------------------------------<br>> >> From: x.periole@rug.nl <mailto:x.periole@rug.nl><br>> >> To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org><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 <br>> >> question maybe somewhat<br>> >> naive. My objective is to run a few steps of <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 <br>> >> the<br>> >> .mdp file provided in this procedure. The <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 <br>> >> creating a<br>> >> low coloumb energy score after minimization/molecular dynamics<br>> >> (check by looking at the log-file). However, a covalent bond <br>> >> is<br>> >> being created between them instead. This should not be <br>> >> happening. What do you mean a covalent bond is being created! <br>> >> This is basically<br>> >> not possible! Would that just be a visualization effect? <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, <br>> >> please let me know, and<br>> >> thank you in advance.<br>> >> Abdullah Ahmed <br>> >> ------------------------------------------------------------------------<br>> >> Hotmail: Free, trusted and rich email service. Get it now.<br>> >> <https://signup.live.com/signup.aspx?id=60969> -- <br>> >> gmx-users mailing list gmx-users@gromacs.org<br>> >> <mailto:gmx-users@gromacs.org><br>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> >> Please search the archive<br>> >> at http://www.gromacs.org/search before posting!<br>> >> Please don't post (un)subscribe requests to the list. Use <br>> >> the www interface or send it to gmx-users-request@gromacs.org<br>> >> <mailto:gmx-users-request@gromacs.org>.<br>> >> Can't post? Read http://www.gromacs.org/mailing_lists/ <br>> >> users.php<br>> >> <br>> >> ------------------------------------------------------------------------<br>> >> Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. <br>> >> Sign<br>> >> up now. <https://signup.live.com/signup.aspx?id=60969> -- <br>> >> gmx-users mailing list gmx-users@gromacs.org<br>> >> <mailto:gmx-users@gromacs.org><br>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> >> Please search the archive at http://www.gromacs.org/search before<br>> >> posting!<br>> >> Please don't post (un)subscribe requests to the list. Use <br>> >> the www interface or send it to gmx-users-request@gromacs.org<br>> >> <mailto:gmx-users-request@gromacs.org>.<br>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> >> ------------------------------------------------------------------------<br>> >> Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign <br>> >> up now. <https://signup.live.com/signup.aspx?id=60969><br>> ><br>> > -- <br>> > ========================================<br>> ><br>> > Justin A. Lemkul<br>> > Ph.D. Candidate<br>> > ICTAS Doctoral Scholar<br>> > MILES-IGERT Trainee<br>> > Department of Biochemistry<br>> > Virginia Tech<br>> > Blacksburg, VA<br>> > jalemkul[at]vt.edu | (540) 231-9080<br>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> ><br>> > ========================================<br>> > -- <br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before <br>> > posting!<br>> > Please don't post (un)subscribe requests to the list. Use the www <br>> > interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />Hotmail: Trusted email with Microsoft’s powerful SPAM protection. <a href='https://signup.live.com/signup.aspx?id=60969' target='_new'>Sign up now.</a></body>
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