[gmx-users] Unneccessary bonding

abdullah ahmed abdullah_renk_ahmed at hotmail.com
Mon May 3 17:52:16 CEST 2010

Thank you very much for your reply, 
I agree it is probably a visualization of the effect, and that there is no bond. However, the distance between the two atoms participating in this "phantom bond" is 1.4 A°. Isn't that too close? Shouldn't it be considered a clash? 


From: x.periole at rug.nl
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Unneccessary bonding
Date: Mon, 3 May 2010 17:36:29 +0200

On May 3, 2010, at 5:16 PM, abdullah ahmed wrote:Hello, 

I am a new user to GROMACS and so this question maybe somewhat naive. 

My objective is to run a few steps of minimization on a PDB structure and then obtain the energy value. To do so I ran the procedure suggested in the tutorial called "speptide" using the .mdp file provided in this procedure.   

The structure I am using has two oppositely charged residues facing each other. The initial distance(3.2 A°) is such that ionic interactions should occur between them, thereby creating a low coloumb energy score after minimization/molecular dynamics (check by looking at the log-file). However, a covalent bond is being created between them instead. This should not be happening. 
What do you mean a covalent bond is being created! This is basically not possible! Would that just be a visualization effect? This could result from the fact that the two atomsget really close to each other and thereby your visualization program thinks it is a covalentbond.

Does anyone have any ideas on what may be happening and how I can fix it? 

If this information is not sufficient, please let me know, and thank you in advance.

Abdullah Ahmed 

Hotmail: Free, trusted and rich email service. Get it now. -- 
gmx-users mailing list    gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Your E-mail and More On-the-Go. Get Windows Live Hotmail Free.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100503/5ae00b65/attachment.html>

More information about the gromacs.org_gmx-users mailing list