On Sat, Dec 29, 2007, Wei Chen wrote:
>
> 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.
The instructions on the antechamber web page should produce RESP charges,
rather like those in ff94 and ff99. The charge model used for ff03 is
different (see the paper describing it for details). So, you should compare
your charges with those in all_amino94.in.
[Other know more about this stuff than I do, but I hope this gets you pointed
in the right direction, and that others on list will correct any
mis-statements I have made.]
...dac
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Received on Sun Dec 30 2007 - 06:07:37 PST
