Re: [AMBER] Protonation of C terminal residue

From: FyD <>
Date: Thu, 24 Feb 2011 13:12:06 +0100

Dear Elisa,

> I need protonation state on Serine C-term. I would like to ask you how I can
> do this and there is a good lib that I can use.

The protonation state of the COOH group of Serine does not exist in
solution at pH~7. Thus, a better option to model a neutral Serine
might be to cap it with a NHMe group (NME).

Anyway, if you need this COOH-fragment, you could follow two approaches:

1) The first approach is summarized .

You follow a similar approach simply replacing MeCOO(-) by MeCOOH
You can find examples of such an approach in R.E.DD.B.; see for instance:
  Java applet

2) The second approach can be adapted from the 'Central-fragment'
procedure summarized .

However, you apply a single intra-molecular charge constraint
(INTRA-MCC keyword in a P2N file) on the CH3CO capping group (ACE) and
you do not use any NHMe group:

              A single INTRA-MCC set to zero

In fact, I would test the case 2) first, and then the case 1)

You also need to decide which phi, psi & chi dihedral angle values you
wish to use to define your conformation(s)...

The whole process can be automatically carried using R.E.D.-III.4 or
R.E.D.Server/R.E.D. IV.

regards, Francois

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Received on Thu Feb 24 2011 - 04:30:09 PST
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