Hello everyone,
I have two protein structures, and the insides of both are not exposed to
water.
One structure contains two oppositely charges residues (GLU and LYS) facing
each other. The second structure contains a GLU residue only.
Upon minimization I had expected the coloumb energies of the first structure to
be lower than that of the second. However, this was not the case, they are both
very similar.
Does anyone have an idea as to why this has happened?
(The only explaination I can come up with is that perhaps the effect is so
small that it can not be seen)
I was not sure if providing PDB and .mdp files would be helpful, but I can send
then in my next mail if neccesary.
Thank you in advance!
Abdullah Ahmed
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