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.
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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