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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