AMBER Archive (2007)

Subject: Re: AMBER: xLeap "Could not find type" error

From: David A. Case (case_at_scripps.edu)
Date: Wed Aug 22 2007 - 10:45:02 CDT

On Wed, Aug 22, 2007, WANG,YING wrote:

> created a new atom named: H within residue: .R<NPHE 1>

You pdb file has an atom named "H" in the first residue, but there is no such
atom in the N-terminal residues in the Amber libraries. You need to match up
the atom names in the pdb file with the Amber ones; in this case, the easiest
thing is to remove this H atom from the pdb file.

> The file contained 17 atoms not in residue templates

You didn't show any of the other errors, not provide the pdb file you used,
so there are probably other naming inconsistencies as well. As a guess, you
might need to run protonate on you pdb file.

...dac

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