Re: Re: [AMBER] force field with neutral terminal

From: Jason Swails <>
Date: Wed, 17 Mar 2010 11:16:40 -0400

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 M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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Received on Wed Mar 17 2010 - 08:30:07 PDT
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