Re: AMBER: creating residues - charge assign problems

From: FyD <>
Date: Fri, 13 May 2005 17:25:48 +0200

please see:
for instance:

search using RESP ESP charge Derivation with google .
selecting mailing list mailing list archives

This has been many times discussed.
Regards, Francois

> I am in the process of creating a number of units that I hope to combine
> together to form a single macromolecule. I have built each residue using
> xleap, and fitted the charges to each atom using Gaussian followed by resp.
> However, I am having trouble knowing how to deal with connect atoms.

See also the Cieplak et al J. Comput. Chem 1995, 16, 1357-1377

> My strategy so far has been this:
> 1. Build the residue connected to a number of extra atoms so that the
> charges for the connect atoms are realistic
> 2. Once charges have been assigned, cut the extra atoms off
> 3. Save the remaining atoms within the molecule as a prep file or OFF
> file
> The problem is:
> If I cleave off the extra atoms, I get a charge of about +0,6 for the unit.
> This isn't ideal. It seems to me that the alternative is to perform Gaussian
> charge assignment with a "floating" connect atom. However, on performing
> both charge assignments (i.e "floating" and "cutting off atoms") I get
> rather different charges for the connect "O" atom and for those atoms in the
> immediate vicinity of the connect atom.
> I'm rather new to this whole antechamber/residue creation business. As such,
> a few questions:
> 1. Am I misunderstanding this procedure?
> 2. If not, which of the 2 strategies is the lesser of evils?
> i. i.e. "floating"
> type calculation: no net charge for unit but inaccurate connect atom charges
> ii. "cutting" type
> calculation: accurate connect atom charge but overall residue charge is
> non-zero
> 3. The system I am looking at will ultimately be used to simulate a
> possible docking event with a substrate protein. I will therefore be looking
> at non-covalent interactions. Is there a rule of thumb with a large system
> like this as to which of the above strategies I use?

  F.-Y. Dupradeau
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
The Scripps Research Institute, La Jolla, CA, USA
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Received on Fri May 13 2005 - 16:53:00 PDT
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