Re: [AMBER] Prepping PDB files for amber

From: Lachele Foley (Lists) <"Lachele>
Date: Mon, 19 Dec 2011 16:39:10 -0500

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:

We're working on an updated and smarter version. Other folks might
have tools, too.

On Mon, Dec 19, 2011 at 4:16 PM, Jeffrey Thalhammer
<> wrote:
> Disclaimer:  I am a software engineer, so please excuse me for any ignorant questions or misused terminology.
> I am architecting a research pipeline using Amber.  According to the tutorial in the amber manual...
> ...[Most] PDB files needs some editing before it can be used by Amber...Although Amber tries hard to interpret files in PDB formats, it is typical to have to do some manual editing before proceeding. A general prescription is: "keep running the loadPdb step in 16LEaP (see step 2, below), and editing the PDB file, until there are no error messages."
> The tutorial mentions selecting alternate conformations of certain residues, removing phosphate groups and water molecules, changing CYS to CYX as examples of the "edits" that are required before feeding a PDB to Amber.  My question is whether anyone has packaged these common edits into a tool that can be used pre-process PBD files.  A secondary question is why Amber doesn't do these transformations itself, if they are as common and systematic as the tutorial suggests (given that PDB is standard format).
> Thanks for your time.
> -Jeff
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Mon Dec 19 2011 - 14:00:03 PST
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