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

From: Jason Swails <>
Date: Fri, 25 Mar 2011 14:01:19 -0700

Hmm... I was just talking to a colleague about this, actually. Add 'LYN' to
the list of residues in $AMBERHOME/src/sander/rgroup.f . Search for any
other standard amino acid (i.e., "ASP") to find out where in the file you
should make that modification.

I'm not completely positive what the decomp code does, but in any case, try
that out and see what happens.

Don't forget to recompile after you've made this change or you won't see

Good luck,

On Fri, Mar 25, 2011 at 10:34 AM, Rubben Torella

> 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
> simulations.
> 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
> Rubben
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Fri Mar 25 2011 - 14:30:02 PDT
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