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.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of FyD
Sent: Wednesday, June 10, 2009 11:48 PM
To: amber.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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 06 2009 - 10:02:50 PDT
