[gmx-users] Unneccessary bonding

XAvier Periole x.periole at rug.nl
Mon May 3 17:36:29 CEST 2010

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 atoms
get really close to each other and thereby your visualization program  
thinks it is a covalent
> 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
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