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

From: Rajesh Raju <>
Date: Tue, 22 Feb 2011 16:27:30 -0600

Dear , Francois,

I have attached the molecule in jpg format. The system is a salt whose
charge is neutralized by 4 Br- anions. I have a couple of questions:

[1] Do I need to include the Br- anions in making the paramter file..,
but the exact position of the Br- is unknown...

[2] when I optimize at HF/6-31G*, do i need to include the Br- anion..

Also from literature, Br- aninons helps to maintain the stacked form
of the two pyrene rings,
But when I optimzed, without Br- aninons, the molecules moving away..

Rajesh Raju

On Sun, 20 Feb 2011 17:52:57 +0100
  FyD <> wrote:
> 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
>> Thank you very much for your reply. I have not performed any
>> 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
> by the program?
> You can quickly check chemical equivalencing for your _whole_
> 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 &
> R.E.D. Server/Ante_R.E.D. 2.0 to generate a P2N file (it will take
> sec); (iii) use the Java applet to display the atom names of the P2N
> file.
> Chemical equivalencing is reflected by the first column of atom
> in a P2N file: two chemically equivalent atom should bear a same
> 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
>> 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.
> 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
>> My molecules contains 2 pyrene rings, 4 charded imidazole rings, and
>> a briged benzene rings. All the molecules are conncted through
>> 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.
> See
> I hope this helps.
> regards, Francois
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Received on Tue Feb 22 2011 - 14:30:04 PST
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