Re: [AMBER] Removed proton in proteins

From: case <>
Date: Mon, 8 Mar 2010 10:25:20 -0500

On Mon, Mar 08, 2010, Francesca Cantini wrote:
> I would like to ask you if it is appropriate and/or necessary to
> remove all protons in the pdb before running LEAP.

It often helps, since hydrogen names in PDB files may or may not match
those in the Amber libraries.

Part of this arises from the fact that the PDB recently updated all its files
(to "version 3.x") with new hydrogen names. Part of it comes from the fact
that many programs create "PDB" files, and they do not always adhere to

Current Amber programs should read in current (version 3) PDB files without
problems. But if you do see problems, the simplest solution is often just to
remove the hydrogens from the PDB file and let LEaP rebuild them. If you
don't want to do this, then you will need to edit your PDB file so that the
atom names match those in the Amber libraries. A program like "reduce"
may also be of great help here:

...hope this helps...dac

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Received on Mon Mar 08 2010 - 07:30:04 PST
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