AMBER Archive (2009)

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

From: Aust, Susanne (saust_at_ipb-halle.de)
Date: Mon Oct 19 2009 - 04:01:27 CDT

I think, you must change the name for the GLU in the pdb to GLH (see in xleap
the list of amino acids), then your GLu has a hydrogen on one oxygen.
Susanne

-----Ursprščngliche Nachricht-----
Von: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org]Im Auftrag
von xuemeiwang1103
Gesendet: 14 October 2009 14:06
An: amber
Betreff: [AMBER] Add the hydrogen to the carboxyl of the GLU residue?

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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