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
bond.

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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