Re: [AMBER] Probelm with antechamber for resp charge derivation

From: FyD <>
Date: Sun, 20 Feb 2011 17:52:57 +0100

Dear Rajesh Raju,

The problem is not that a program can generate a set of charges or
not. The problem I wanted to underline is that for such a large &
multiply charged molecule the conformation obtained after geometry
optimization is likely to be different to what it is in a solvent or
docked in a protein...

The conformation between multiple cycles is another problem in your case...

> Thank you very much for your reply. I have not performed any building
> block approach for resp charge derivation. I have checked the
> geomtery. It is a symmetric molecule, with a bridged benzene ring.

Another key problem in this type of 'symmetric' molecule is charge
equivalencing for chemically equivalent atoms: is it correctly applied
by the program?

You can quickly check chemical equivalencing for your _whole_ molecule
using R.E.D. Server:

(i) prepare a PDB file of your structure (with a correct input
geometry to get a quick result); (ii) upload your PDB input file & run
R.E.D. Server/Ante_R.E.D. 2.0 to generate a P2N file (it will take few
sec); (iii) use the Java applet to display the atom names of the P2N
Chemical equivalencing is reflected by the first column of atom names
in a P2N file: two chemically equivalent atom should bear a same name,
and after charge derivation they should bear the same charge value
(when one uses R.E.D.)...

> Can I use RED programme for derving such large molecules..If so can u
> suggest, the best tutorial for me to follow. I have not used RED
> before.

R.E.D. & now R.E.D. Server have been developed for RESP & ESP charge
derivation and force field library building. R.E.D. IV & R.E.D. Server
handle quite complex charge derivation by now, and obviously the
building block approach first defined in the following paper:

> I am have used antechamber quite oftern for small molecules. Is it
> posssible building block approach for antechamber?

I guess by running antechamber, adapting RESP inputs manually &
correctly concatenating espot files and re-running antechamber, it
should be possible...
The problem here is that one needs to understand the different steps.

> My molecules contains 2 pyrene rings, 4 charded imidazole rings, and
> a briged benzene rings. All the molecules are conncted through -ch2
> groups. the molecule is symmetrical w.r.t benzene ring. it would be
> helpful if anyone can suggest a best way to derive charge..

This is difficult to help without a picture of your molecule; Could
you send a drawing for your molecule? However you might look at the
calixarene project in R.E.DD.B. by E. Vanquelef. I am sure you will
find ideas for your own project.

I hope this helps.

regards, Francois

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Received on Sun Feb 20 2011 - 09:00:04 PST
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