AMBER Archive (2009)

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

From: Carlos Simmerling (
Date: Wed Oct 14 2009 - 08:49:00 CDT

I think the mention of "FFTopDB" is a bit confusing- GLU and GLH are indeed
available in the standard Amber libraries so there is no need to go to
anything other than your Amber directory. if you load the leaprc file as
directed in the manual, (such as leaprc.ff99SB, then GLU and GLH work just
fine. As Andrew posted, rename the residue to GLH if you want it protonated.

On Wed, Oct 14, 2009 at 9:40 AM, FyD <> wrote:

> Hello,
> 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!
> When you use LEaP you generally first load a set of FF libraries and then
> your PDB file. LEaP recognizes your PDB file only if a match is observed
> between the FF libraries loaded and your PDB file.
> For each residue found in a PDB file, you potentially need a specific FF
> library. This means that for the central fragment of an amino-acid for
> instance you need to have a match between your amino-acid residue in your
> PDB file and a FF library. Match means same residue name & same atom names
> in the PDB file and in the FF library. Moreover, if some atoms (not only
> hydrogens - works also for heavy atoms) are missing in the PDB file for the
> considered residue, these missing atoms can be added in LEaP _only if_ a
> match is found (once again) between the PDB file and the FF library.
> Let's take an example:
> - You first load the FF library of the central fragment of the ALA
> amino-acid//residue in LEaP - it belongs to the Amber force field topology
> database (FFTopDB), no problem.
> - You then load a PDB file with this ALA central fragment of Alanine
> somewhere in the middle of your protein.
> The recognition between your PDB and your FF library will append only if
> you have the same residue name (i. e. ALA) and the same atom names (i. e. N
> H CA HA CB HB1 HB2 HB3 C O) in the PDB file and in the FF library. Now if
> some atoms are missing in the PDB file for this ALA fragment, for instance
> the methyl beta (4 atoms), the corresponding atoms will be automatically
> added in the PDB file by LEaP - if - once again a match is found between the
> PDB file and the FF library.
> In your case, if you have a PDB file with the GLU residue; GLU means delta
> COO(-) in your PDB file, you will need to load first the FF library for this
> GLU residue in LEaP. No problem it is available in the Amber FFTopDB.
> If you want a PDB file with the GLH residue; GLH means delta COOH in your
> PDB file, you need to have a FF library for this GLH residue. Check in the
> Amber FFTopDB if it is available. It might not. If not, you need to create
> your own force field libraries for the central fragment of this amino-acid
> (and may be for the N-terminal & C-terminal fragments as well).
> For creating FF libraries for new amino-acid fragments you could use
> R.E.D.-III.3:
> See
> To interface R.E.D. IV:
> See R.E.D. Server @
> & the corresponding tutorials @
> See in particular:
> as well as:
> You will also find examples of amino-acid fragments in R.E.DD.B.
> See for instance:
> for the ff99SB force field or
> for the ff03 force field.
> I hope this helps.
> regards, Francois
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