AMBER Archive (2009)

Subject: Re: [AMBER] Add the hydrogen to the carboxyl of the GLU residue?

From: Andrew Purkiss-Trew (
Date: Wed Oct 14 2009 - 07:19:43 CDT

Just rename your GLU 347 residue to GLH in the pdb file. GLH gives the
protonated form of the sidechain, whilst GLU give the more normal
unprotonated form.

On Wed, 2009-10-14 at 20:05 +0800, xuemeiwang1103 wrote:
> Hi:
> I am very sorry for ask the the same question again ,because I didn't solve the problem until now . Once again,the leap can automaticaly add the missing hydrogen to the protein seq.As we kown ,the GLu residue has two carboxyls ,one of them formed piptide bond ,the other was charged -1 and wasn't added the hydrogen by leap.Now if I want to add the hydrogen to the carboxyl to make the only Glu347 neutraled ,How should I do this ? Could I create a new residue by using Anttechamber command ,however it seems complexed and I didn't successed by using this method .Thanks again!
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Andrew Purkiss-Trew
X-ray Laboratory
London Research Institute
Cancer Research UK

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