THank you Jason for your help.. now it seems to work!
I was wondering why this option is not just implemented in the code..
thank you again
Rubben
2011/3/25 Jason Swails <jason.swails.gmail.com>
> 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
> anything.
>
> Good luck,
> Jason
>
> On Fri, Mar 25, 2011 at 10:34 AM, Rubben Torella
> <rubben.torella.gmail.com>wrote:
>
> > 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
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> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
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Received on Tue Mar 29 2011 - 04:00:03 PDT
