AMBER Archive (2004)

Subject: Re: AMBER: charge not zero

From: FyD (
Date: Wed Aug 04 2004 - 14:57:51 CDT

Dear Anshul,

First, I finally finish to summarize the FAQ for R.E.D.-I.
See on the R.E.D. Web site
> 1. What i want to do is that, I have to replace some of the aminoacids
> from a protein with another aminoacid which is attached with an organic
> molecule (lets name this unit as x). Now I prepare the prepin file for
> this unit (x). the end group in this unit (end of the aminoacid part) is
> protectd with NH Me and ACE. now when i replace the orignal amino acid
> with this unit, what should i do to the end group. Should it be emoved and
> if yes then do i need to make some adjustments in the charges after its
> removal.

If I understand you, you have a new residue AAX. In your protein, it should
have the following form -NHCH"X"-, if it is a 'central' AA i.e.

To get the charges for such systems, you could use the capped model below as it
is described in the Ciepak et al. J. Comput. Chem. 1995 16 1357-1377:

It is better to select phi,psi dihedrals describing 2/3 different
conformations. For instance, one in the canonical alpha helix, and another one
in the canonical beta-sheet.
See once again the Cieplak et al. paper...
See also:

I guess it is better to apply multi-conformational and multi-orientation RESP
fit in this case. I can provide you R.E.D.-II to do this if you want... For me,
R.E.D.-II is ready, now, until the next bug is found ;-) I still have to update
the manual...

- You select 2/3 conformations based on the Cieplak et al paper or based on
some ideas you have about your system and let's say you select 4 orientations.
You run R.E.D.-II and you get the charges for this CH3CO-NHCH"X"-NHMe

- You copy the 'espot' (contains the espot$i*$j, $i=conformations,
$j=orientations), 'input1' and 'input2' files obtained in a new directory.

- You add restaints to put to total charge of your CH3C0- and NHMe- groups =
zero in the 1st RESP input and you freeze them in the 2nd RESP input (i.e. =

- You modify manually the 'input1' and 'input2' and you run the 2 aliases
provided at:

- You have your charges for your central AAX i.e. -NHCH"X"- in the new punch2
file generated after running RESP manually... The total charge for -NHCH"X"- is
then obviously = zero...

- You create a Sybyl file for -NHCH"X"- (using 'insightII' for instance). The
conformation of this AAX is NOT important and does NOT matter at this stage.
ONLY the RESP charges describing different conformations & orientations

- You add manually (text editor or in insightII) the RESP charges (and atom
types describing your FF) in this file selecting only the RESP charges of
-NHCH"X"- from the new punch2 (i.e. the charges of CH3CO- and -NHMe are not
used anymore).
See to known which columns to

With R.E.D.-III, the FF atom types will be automatically recognized and added in
the Tripos format...

- You load this .mol2 file in amber8/xleap

M = loadmol2 AAX.mol2

You have a new '' library which describe your new central AAX ready to
loaded with a 'loadoff' command in a leaprc.ff99 file when you will
to load your whole protein-PDB file containing this new AAX....

I am writting this tutorial... It should come up beginning of next September...

> 2. Should my end group contain the end group or not?

? ...

> 3. Presently I am replacing the aminoacid in InsightII. I manually remove
> the orignal amino acid and then form a bond with this unit. I would like
> to know if there is any other simpler method to do so.

I use also InsightII to build starting structures and switch to xleap/sander to
recognize/run simulations...

In insightII, 2 advice:

-1 Save your PDB/mol2 files without the hydrogens (if possible),
'xleap' will add them automatically. The atom name of the hydrogens generated
by 'insightII' are often not recognized by 'xleap'...

-2 Be sure that the 'atom name' and 'residue name' of each AA (not only AAX) in
the file generated by insightII match the corresponding 'names' in the xleap
.off libraries...

And it will work... Regards, Francois

Such whole protocole will also be implemented in R.E.D.-III...
PERL is great for such protocoles which are very simple to implement when we
have understood all the different steps...

F.-Y. Dupradeau
Faculte de Pharmacie, UPJV, Amiens, France
The Scripps Research Institute, San Diego, USA
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