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

From: FyD <>
Date: Wed, 21 Mar 2012 08:02:44 +0100

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.

You do not need to register to use Ante_R.E.D. 2.0 at R.E.D. Server:

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 - 00:30:02 PDT
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