AMBER Archive (2009)

Subject: Re: [AMBER] RED: Charge derivation of transtion state analogue

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sun Jul 05 2009 - 04:39:13 CDT

Dear Manoj Singh,

> I am trying to study binding properties of one substrate and
> its transition state analogue in Amber10.
>
> I derived charges of the substrate in RED-III, using its single orientation
> and single conformation.
>
> For transition state analogue I have change the bond length of partial
> breaking bonds and constraint the partial formed bond distance using
> distance based restrain, consistence to the previous quantum study for the
> reaction mechanism (method is similar to Angw. Chem. Int. Ed. Volume 45
> Issue 4 <http://www3.interscience.wiley.com/journal/112226663/issue>,
> Pages 653 - 657,
> used with other system). I ran the molecular dynamics of the this system
> to equilibrate the structure according to the new bond lengths at reaction
> center. Now, I want to fit the charges of substrate, water molecule and the
> amino acids taking part in reaction (there are two amino acid and a water
> molecule along with substrate forms the reaction center). I want to retain
> the bond lengths of partial bands during the charge fitting process.
>
> I will be very thankful if some one can guide me through this charge fitting
> process in RED-III.

You need to:
-1 define the atoms to be involved in the charge derivation process in
a PDB file (input of Ante_R.E.D.); let's called it "your complex".
-2 execute Ante_R.E.D. to generate the QM input for the geometry
optimization step & the P2N file for R.E.D.
-3 using the QM input generated by Ante_R.E.D., run the QM geometry
optimization step in a standalone approach (i.e. without R.E.D.).
-4 You check the P2N files: in particular, are the connectivities
defined as you want they reflect the molecular topology of your complex.
-5 You rename the file generate in -3 into "Mol_red1.log" + the file
generate in -4 into "Mol_red1.p2n". You ran R.E.D.-III.x (or R.E.D.
Server) using $OPT_Calc = "Off" & $MEP_Calc = "On"; i.e. using the
"mode 2".
See http://q4md-forcefieldtools.org/REDS/popup/popmodes.php

* If you want to fix a bond, you need to do it during the geometry
optimization step using specific keyword/constraint in the QM program.

* If you want to fix some charge values in the fitting step, you need
to add the INTRA-MCC keyword in the corresponding P2N file.

* You might represent your amino-acids by their dipeptide versions
(ACE-AA-NME), to remove the 2 capping groups using the INTRA-MCC
keyword and setting constraints to zero for these chemical groups.

In fact, you have to apply exactly the same strategy for this complex
than that
you applied to generate the charges for your transition state
structure: there is no fundamental difference. Pay also attention to
charge equivalencing for chemically equivalent atoms (or atoms you are
going to consider equivalent) in such a complex case (This is defined
in the 1st column of atom names in the P2N file format).

Do not hesitate to ask more questions as this example is quite
complex/interesting...

regards, Francois

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