AMBER Archive (2009)

Subject: Re: [AMBER] non standard residue

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Tue Jul 07 2009 - 02:50:09 CDT

Dear Neha,

> I have a protein structure (protein.pdb) and it has a residue called ACA in
> chain C. I have prepared lib file (ACA.lib). Then I describe head and tail
> group of this non standard residue. I saved the file as ACA.lib. I m yet to
> calculate the charges.
>
> I try to load the whole protein after loading the lib file. The N-terminal
> of ACA residue connects well with the previous residue but the C-terminal of
> this residue misses out the connectivity with the N atom of the proceeding
> residue which is MET.

Here you have to well define the head & the tail for your new peptide
fragment in your LEaP script. See for instance this example:
http://q4md-forcefieldtools.org/Tutorial/P2N/All-frag-Pept/script1.cmd

For the charge derivation of amino-acid fragments & force field
library building, you can look at:
http://q4md-forcefieldtools.org/Tutorial/
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#16
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24

> Well, this residue is connected at the ends with standard amino acid and
> hence if I use the gaff forcefield, it complains about the atom type between
> standard and non standard residue. If I use amber atom type then its
> complains about the N-N bond type wherein no such bond exists in the
> peptide.

Yes I saw examples of such N-N bond in the literature in peptide analogs:
you might look at the work of P. Legrel (Rennes, France)
You need to use the Amber99SB force field/force field atom types.
For this N-N bond, you will have to develop your own FF parameters.

regards, Francois

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