On Wed, Mar 06, 2013, Nan Li wrote:
> I used xleap to add hydrogens to peptides (the peptide was loaded as
> pdb file without hydrogens) automatically. For the -COOH groups in the
> c-terminal, the Hydrogen is not added (the peptide ends with -COO). Is
> there any reason for xleap not to add hydrogen atom to -COO?
> Also, I checked the charge that is zero. Thanks a lot.
Amber doesn't have amino acid libraries with a neutral COOH end group, so if
you need this (e.g. for peptides under very acidic conditions), you will have
to build them yourself. It's not all that hard, since neutral carboxylate
groups are present in ASH and GLH -- you would have to adapt the atom types
and charges there to the C-terminal residues.
I'm guessing(?) your peptide has a zero charge because it is a zwitterion, with
a positive N-terminal residue and a negative C-terminal one (which is
generally appropriate near neutral pH in water).
....dac
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Received on Wed Mar 06 2013 - 18:00:03 PST
