Hi WJ
Take a look at the following tutorial:
http://ambermd.org/tutorials/advanced/tutorial1/
This shows how to do charge derivation for bonded ligands - i.e. how to cap
things so that your residue gets an integer charge etc.
Good luck,
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
WJ Ding
Sent: Thursday, October 30, 2008 9:20 PM
To: amber.scripps.edu
Subject: AMBER: how to ger resp charge for a residue?
Dear all,
I am trying to create the library for a non-standard residue with tleap. I
have created atoms, residue, and unit, and set element, bond and zmatrix.
When I checked the unit, it always said
"ERROR: The unperturbed charge of the unit: 0.190640 is not integral.
WARNING: The unperturbed charge of the unit: 0.190640 is not zero."
The charge for a residue should be integral, right? I calculated the resp
charge for the whole molecular with Gaussian. I know there must be
difference in resp charge bewteen the whole molecule and the residue. My
point is how to
solve this problem? How could I get resp charge for a residue (except
R.E.D.)?
Any help will be highly appreciated. Thanks in advance.
WJ
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Received on Fri Oct 31 2008 - 05:12:44 PDT
