AMBER Archive (2008)

Subject: Re: AMBER: LEaP problem with LEU first residue?

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Oct 15 2008 - 08:18:58 CDT

On Tue, Oct 14, 2008, Francesco Pietra wrote:

>
> What I am asking here is if hydrogens have been added correctly to LEU
> as first residue, focusing the attention to hydrogen names for atoms
> 2-4. From Amber, I would have expected
>
> 2 H1
> 3 H2
> 4 H3
>

The atom names all look correct to me. The PDB standard has recently changed
about how such atom names are encoded in a PDB file. Amber programs *should*
recognize either the new or the old convention. If you need to use these PDB
files with other programs, you may need to do some hand-editing.

...dac

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