[AMBER] Prepping PDB files for amber

From: Jeffrey Thalhammer <jeff.imaginative-software.com>
Date: Mon, 19 Dec 2011 13:16:47 -0800

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.

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Received on Mon Dec 19 2011 - 13:30:02 PST
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