On Tue, Feb 15, 2011, vani panguluri wrote:
>
> while loading the pdbfile it was displaying the following messages
> Created a new atom named: HN within residue: .R<LEU 544>
> Created a new atom named: 1HB within residue: .R<ALA 545>
> Created a new atom named: 2HB within residue: .R<ALA 545>
> Created a new atom named: 3HB within residue: .R<ALA 545>
It looks like your pdb file does not follow standard nomenclature, and may
have the atom names in unexpected columns. First, the amide hydrogen should
be named "H", not "HN". The naming of the hydrogens attached to CB in SER
and ALA also are not being recognized.
One common option is to remove all the hydrogen atoms from the pdb file, and
let Amber re-add them with the proper names.
....dac
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Received on Tue Feb 15 2011 - 16:30:04 PST
