AMBER: creating residues - charge assign problems

From: Hayden Eastwood <>
Date: Fri, 13 May 2005 12:06:06 +0100

Dear Amber users


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.


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


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

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?



Any advice would be much appreciated.




Hayden Eastwood



Hayden Eastwood

Perdita Barran Research Group

Joseph Black Building

Edinburgh University

West Mains Road



Tel: 0131 650 4773


Research page:

"You have to be an academic to believe some things; no ordinary person would
be so stupid." -George Orwell


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Received on Fri May 13 2005 - 12:53:00 PDT
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