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Hello, <br><br>I am a new user to GROMACS and so this question maybe somewhat naive. <br><br> 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. <br><br>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. <br><br>Does anyone have any ideas on what may be happening and how I can fix it? <br><br>If this information is not sufficient, please let me know, and thank you in advance.<br><br>Abdullah Ahmed <br> <br /><hr />Hotmail: Free, trusted and rich email service. <a href='https://signup.live.com/signup.aspx?id=60969' target='_new'>Get it now.</a></body>
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