Re: [AMBER] Prepping PDB files for amber

From: Jeffrey Thalhammer <>
Date: Mon, 19 Dec 2011 14:22:25 -0800

On Dec 19, 2011, at 1:39 PM, Lachele Foley (Lists) wrote:

> The code is getting a little old, so do let me know if you find
> something that doesn't work. But, there is a tool here:

Yes, that's exactly what I had in mind. I see that it does a nice job of removing the hydrogens and zeroing/stripping the columns that Amber doesn't want. But the cysteine residues are still CYS rather than CYX.

Anyway, is the source code available under an open source license? Is there an API or command-line interface? The web interface is slick, but not practical for an automated pipeline.

AMBER mailing list
Received on Mon Dec 19 2011 - 14:30:02 PST
Custom Search