I'm not really sure. In my opinion, any residue in Amber's standard set
should be present, yet none of the "abnormal" protonation states are (i.e.
protonated carboxylates or deprotonated amines). Since this works, I'll go
ahead and add those to the list for upcoming amber releases.
All the best,
Jason
On Tue, Mar 29, 2011 at 3:50 AM, Rubben Torella <rubben.torella.gmail.com>wrote:
> 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Mar 29 2011 - 08:30:03 PDT
