Thanks for the explanations and suggestions. As this is not in real case, my aim was to test whether the end caps (neutral and charged) has any significant role in the formation of secondary structures. I tried with zwitter ion and has the results out of it, so I want to try this.
I have one opinion and I want to know whether its right or not to carry out?
Can I take the CNEU and NNEU from charmm and have the parameters of it as same as in amber (e.g we have COO in amber and to include one hydrogen with parameters same as that in NTER)?
Thanks in advance for any comments/suggestions
Ramya.L.
On Wed, 17 Mar 2010 20:42:31 +0530 wrote
>On Wed, Mar 17, 2010 at 2:59 AM, Ramya Narasimhan
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
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Received on Thu Mar 18 2010 - 22:30:02 PDT
