[AMBER] Neutral Lysine (LYN) not calculated in MM_PBSA

From: Rubben Torella <rubben.torella.gmail.com>
Date: Fri, 25 Mar 2011 17:34:17 +0000

Dear Amber users,
according to the pKa calculated on my complex with different software, one
lysine on my complex seems to be particularly buried and so possibly with
neutral charge.
So, I change the LYS code for that particular lysine to LYN and leap
(FF99SB) built this neutral lysine and I used this to do some MD
Now the simulations are finished, but when I tried to calculate the binding
energy with GBSA decomposed on every residue, this lysine seems not to
interact with any residue of the complex, that is impossible..
I have read that perhaps the LYN code is not recognized.. is it right? Is
there something that I can do to calculate the binding energy including the
neutral lysine?
Thank you very much
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Received on Fri Mar 25 2011 - 11:00:03 PDT
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