AMBER Archive (2009)

Subject: RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid

From: Brothers, Michael Charles (
Date: Thu Jun 18 2009 - 12:38:53 CDT


I've finally got everything set up to run RED-vIII.2, but for some reason it won't recognize the fact that I have PC-GAMESS installed and not GAMESS. I'm running through the bash shell and have a path set to the directory containing pcgamess.exe.

I attached my .p2n file and my file.

Thank you for your previous help, and hopefully this is just a small oversight on my behalf.


Mike Brothers

-----Original Message-----
From: [] On Behalf Of FyD
Sent: Wednesday, June 10, 2009 11:48 PM
Subject: Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid

Dear Michael,

> I am having issues generating an amber force field for a protein

> containing my non-standard amino acid. I generated the helix itself

> in Macromodel and then modified the amino acid to my side chain

> (Cysteine -> Cys + side-chain, labeled DMV in this model).

When you want to develop a force field library for a new amino-acid, you first need to decide which type of FF library you wish to build:
N-terminal, C-terminal or a central fragment.
(Usually, you only need the central fragment).

You could follow what is provided @

Central fragment:

N-terminal fragment:

C-terminal fragment:

and the three together:

In all the cases, you need to prepare a capped amino-acid (AA), such as ACE-AA-NME, and you cannot use the PDB file you sent.

Examples of similar approaches are available in R.E.DD.B.


regards, Francois

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