how can we delete that hydrogen atoms ,can we able to do this by using
amber........
Regards,
Vani
On Tue, Feb 15, 2011 at 6:29 PM, case <case.biomaps.rutgers.edu> wrote:
> 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 - 17:00:03 PST
