AMBER Archive (2009)
Subject: RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid
From: Brothers, Michael Charles (mcbroth_at_sandia.gov)
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.
> 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:
You could follow what is provided @
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.