AMBER Archive (2008)

Subject: RE: AMBER: how to ger resp charge for a residue?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Oct 30 2008 - 23:46:43 CDT

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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
WJ Ding
Sent: Thursday, October 30, 2008 9:20 PM
To: amber_at_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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