AMBER Archive (2009)

Subject: Re: [AMBER] How to add a hydrogen to the residue?

From: case (case_at_biomaps.rutgers.edu)
Date: Wed Oct 14 2009 - 06:51:08 CDT

On Wed, Oct 14, 2009, xuemeiwang1103 wrote:

> As we kown Leap will add the missing hydrogens to the defined
> templates.But it seems that it only add the hydrogens to the backbone
> of the protein.

This is not correct; LEaP will add any hydrogens in the templates that are not
present in the input pdb file.

> If I want to add one hydrogen to the residue,for
> example : add a hydrogen to the R-coo- which do not form peptide bond
> in the residue seq ,how should I do ? Is it like creat a Non-Standard
> residue pre files using the Antechamber command ? Thanks in advance!

You would need to define your own residue for this. You might look at how ASH
is defined, and use that as a guide to adding a hydrogen to the COO- terminus
of a protein. Of course, you would only expect to have this form under quite
acidic conditions.

...dac

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