> 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?
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"
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Received on Wed Jan 02 2008 - 06:07:06 PST
