AMBER Archive (2009)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Jun 11 2009 - 01:48:27 CDT

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 @

http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php

Central fragment:

http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15

N-terminal fragment:

http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#16

C-terminal fragment:

http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17

and the three together:

http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24

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.

See http://q4md-forcefieldtools.org/REDDB/projects/F-81/

     http://q4md-forcefieldtools.org/REDDB/projects/F-82/

     http://q4md-forcefieldtools.org/REDDB/projects/F-73/

regards, Francois

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