AMBER Archive (2006)

Subject: Re: AMBER: brookhaven to amber pdb format

From: David A. Case (
Date: Wed Aug 02 2006 - 09:48:23 CDT

On Wed, Aug 02, 2006, AYTUG TUNCEL wrote:
> Is there any way to convert brookhaven PDB format to AMBER pdb format. Because hydrogen atoms are represented by different nomenclature. for ex:
> in MET hydrogens of CG are represented by HG1 and HG2 but in AMBER format they are HG2 and HG3.

The "protonate" command can do this: use the -k flag to preserve the
locations, but change the names, of the protons in the input file.

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