Re: [AMBER] Prepping PDB files for amber

From: Jason Swails <>
Date: Mon, 19 Dec 2011 19:26:36 -0500

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).

There are a number of issues here which makes such automation difficult.
 First, do you want the crystallographic waters, or not? Second, there are
several residues whose protonation state can differ based on the conditions
you wish to simulate at. For instance, carboxylic acid residues can be
either protonated at low pH or deprotonated at high pH -- the exact
conditions of which are protein- and conformation-dependent. Different
protonation states need to be represented by different residue names within
Amber, since they have a different number of atoms and different charge
sets. However, in the PDB standard, a protonated aspartate and
deprotonated aspartate are both ASP (ASH in amber is the protonated
aspartate, and ASP is deprotonated).

There are more examples of where an automated workflow becomes difficult,
but this is the first that came to mind.


> Thanks for your time.
> -Jeff
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Mon Dec 19 2011 - 16:30:02 PST
Custom Search