Jason's right- I would just add that it doesn't make sense to ionize side
chains but not unblocked termini. I'm not aware of any conditions in the
"real" world that would give this result, and therefore your simulations
won't provide insight into any physical experiment. You need to think about
what you want to learn- sometimes a non-physical system can be useful, but
you need to have a justification for it.
On Wed, Mar 17, 2010 at 11:16 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, Mar 17, 2010 at 2:59 AM, Ramya Narasimhan
> <ramyashree_81.rediffmail.com> wrote:
> > Actually I am working on the structure prediction of the polypeptide. I
> kept the side chains of the peptide as charged ones in explicit water. I
> carried out the intramolecular energy of peptide with neutral terminals (NH2
> and COOH). Now I want to have the same terminals for the calculation of
> intermolecular interaction energy. From CHARMM, I had a force field with
> CNEU and NNEU (NH2 & COOH), but I want the explicit energy term for the
> hydrogen bonding pairs which is favoured by AMBERff. So is it possible to
> have such neutral terminals in amberff?
>
> All of the terminal residues (C-termini and N-termini) besides the
> "caps" mentioned by Carlos previously are in their zwitterionic form.
> It is certainly possible to create neutral termini and use those in
> your simulation instead of the charged (NH3+, COO-) forms, since
> sander/pmemd itself does not prevent you from doing anything you want
> with your parameters, charges, atom numbers, etc. It'll simply run
> the dynamics. That being said, the neutral forms are not supplied for
> good reason, as Carlos pointed out. It would take an extreme pH to
> neutralize one of the groups (high pH for an NH2 and low pH for a
> COOH). The pH required to set a neutral N-terminus will certainly
> deprotonate the C-terminus and vice-versa. I believe the only way you
> can really get away with neutral termini is if you intend to simulate
> in the gas phase, since pKas/etc. are meaningless outside of water.
> In that case, however, the amber charges are derived for
> solution-phase (slightly polarized), so they should formally be
> rederived if this is desired anyway.
>
> Long story short, what you're asking is possible but it is not
> automated so you'll have to put in some work. The ACE and NME/NHE
> neutral terminal residues are far more physical for aqueous
> simulations, so I think it would be best to stick with those.
>
> Good luck!
> Jason
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 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
Received on Wed Mar 17 2010 - 08:30:08 PDT
