AMBER Archive (2007)

Subject: Re: AMBER: RESP charge fitting using antechamber

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sun Dec 30 2007 - 08:54:59 CST

Quoting Wei Chen <cwbluesky_at_gmail.com>:

> I need to prepare a .prep file for a non-standard amino acid residue. I
> followed the procedure in the tutorial
> http://amber.scripps.edu/antechamber/pro4.html. As a test, I generated a
> ACE-VAL-NME tripeptide. Going through all steps with antechamber and
> gaussian 03, I get a prep file for Valine. However, the charge of each atom
> is quite different from that in all_amino03.in. Could anybody tell me what
> the reason is?

You could also look at the tutorials @
http://q4md-forcefieldtools.org/Tutorial/

First of all, charge values in the AMBER force fields are not reproducible:
See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3
& in particular the section:
"General information about molecular orientation and charge values"

For information about the Duan et al. FF see:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#7

To compute charge values for central & terminal fragments see:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#11

regards, Francois

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