Re: [AMBER] charges for ion and surrounding residues at the active site

From: Jorge Iulek <>
Date: Wed, 21 Mar 2012 13:07:08 -0300

Merci, François, for the new advices.


On Wednesday 21 March 2012 04:02 AM, FyD wrote:
> Dear Jorge,
>> I understand
>> is the *route to go* and programs Ante_R.E.D.-1.x& R.E.D. III.x should
>> suffice (besides the amber programs, of course). Now I should study and
>> apply the mentioned tutorial.
> The global strategy is at:
> Ante_R.E.D. R.E.D. LEaP
> PDB ---> P2N ---> mol2 ---> prmtop/prmcrd
> Concerning the generation of the P2N file(s) you better use R.E.D.
> Server/Ante_R.E.D. 2.0 as only the version 2.0 does handle chemical
> equivalencing between different group of atoms. Ante_R.E.D. 1.x is
> only useful is some particular cases.
> See
> You do not need to register to use Ante_R.E.D. 2.0 at R.E.D. Server:
> See
> Concerning the differences between R.E.D.III.51 and R.E.D.
> Server/R.E.D. IV; see the logos "R.E.D.-III.x compatible"&
> "R.E.D.-III.x incompatible" in yellow color at
> regards, Francois
>> On Tuesday 20 March 2012 08:55 AM, FyD wrote:
>>> Dear Jorge,
>>> You need to extract the "active site" from the protein; this
>>> 'extracted' active site is a 'part' of the protein i.e. a _molecular
>>> fragment_.
>>> A molecular fragment does not exist in quantum mechanics (QM); so this
>>> molecular fragment as to be transformed (using well chosen capping
>>> groups) into a _whole molecule_ for the geometry optimization (i) and
>>> MEP computation (ii) steps performed by QM. Then, during the charge
>>> fitting step (iii) specific charge constraints (intra- and/or
>>> inter-molecular charge constraint(s); See
>>> are used to generated the
>>> wanted _molecular fragment_, which was originally extracted from the
>>> protein.
>>> Key points are:
>>> - checking that the optimized geometry generated during the geometry
>>> optimization (i) using the capped molecular fragment is similar to
>>> that in the protein. Here, you can test different capping group
>>> approaches and/or use geometrical constraint(s) during the geometry
>>> optimization (i).
>>> - comparing the charge values in presence and in absence of these
>>> intra- and/or inter-molecular charge constraint(s) during the charge
>>> fitting step so that these constraints do not impact 'too much' the
>>> charge fitting step (iii).
>>> R.E.D. generates the required molecular fragment(s) in the mol2 file
>>> format (FF library) starting from P2N input file(s) (where the pieces
>>> of information required to build the wanted fragment are provided by
>>> the user; see
>>> At the end, this FF library is loaded in the LEaP program with the
>>> Amber Force Field Topology DataBase to be able to generate the
>>> prmtop/prmcrd files for the entire protein.
>>> See
>>> all these are only generalities ;-)
>>> regards, Francois
>>>> I have a protein to which I wanted to make some molecular dynamics
>>>> and co-factor binding energy calculations. Nevertheless, the active site
>>>> has a Calcium ion. I refer to i) J Mol Biol. 2007 February 16; 366(2):
>>>> 687-701; ii) Journal of Structural Biology Volume 157, Issue 3, March
>>>> 2007, Pages 444-453; iii) J Chem Phys. 2010 Apr 7;132(13):131101; which,
>>>> in general, suggest that more properly the charges for the ion and the
>>>> surrounding residues (including the co-factor?) should be improved with
>>>> a QM calculation beforehand. Also, I see the tutorials a)
>>>> ; b)
>>>> and c)
>>>> . As far as I
>>>> understand, I should submit to a QM program an excerpt of the protein,
>>>> id est, the ion and the closest (complete to the N and C=O) residues
>>>> (maybe any residue which is within 6 A from the ion - so I have a
>>>> molecular fragment(s)) and then get from the QM program the modified
>>>> parameters for them all (including charges). What I could not figure
>>>> still clearly is a step by step tutorial to do this. For this kind of
>>>> molecular fragment (ion + surrounding residues - which most are not
>>>> connected to each other) might the tutorial
>>>> fulfill all
>>>> requirements? In this case it does not resort to Gaussian, should this
>>>> be enough to parametrize the residues and ion to be incorporated into
>>>> the force filed and do the dynamics? I would be happy to read further
>>>> references and tutorial on how to do this.
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Received on Wed Mar 21 2012 - 17:30:03 PDT
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