Re: [AMBER] Prepping PDB files for amber

From: Jeffrey Thalhammer <>
Date: Mon, 19 Dec 2011 22:15:00 -0800

On Dec 19, 2011, at 4:26 PM, Jason Swails wrote:

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

Yes, thanks for the excellent explanation. I'm actually wrestling with the protonation issue too.

Our current pipeline involves manual editing and/or ad-hoc shell scripts to transform the PDB file before handing off to leap. But this just isn't very scalable. I'm sure other folks are going through similar steps, so I'm hoping there are some canned solutions for at least part of the problem (like Lachele has). Or do most people really cook their PDB files by hand?

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Received on Mon Dec 19 2011 - 22:30:02 PST
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