AMBER Archive (2009)

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

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

Francois,

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 RED-vIII.2.pl file.

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

Best,

Mike Brothers

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf Of FyD
Sent: Wednesday, June 10, 2009 11:48 PM
To: amber_at_ambermd.org
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 @

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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