AMBER Archive (2009)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Oct 14 2009 - 08:40:09 CDT

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 http://q4md-forcefieldtools.org/RED/
To interface R.E.D. IV:
See R.E.D. Server @ http://q4md-forcefieldtools.org/REDS/
     & the corresponding tutorials @
http://q4md-forcefieldtools.org/Tutorial/

See in particular:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#13
     as well as:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24

You will also find examples of amino-acid fragments in R.E.DD.B.
   See for instance:
http://q4md-forcefieldtools.org/REDDB/projects/F-75/
   for the ff99SB force field or
http://q4md-forcefieldtools.org/REDDB/projects/F-78/
   for the ff03 force field.

I hope this helps.

regards, Francois

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