On Sat, Oct 09, 2004, MURAT CETINKAYA wrote:
>
> I have a non standard residue (GFP chromophore) that I should build with
> antechamber. If I try gaff parameters, I get the prepin file but head and
> tail atoms are not the ones I want (I get an O atom instead of N and some
> side chain C atom instead of the backbone C atom). So, I cannot build my
> protein using this residue and other standard resiues.
There is a detailed example of creating an amino-acid like residue (with the
proper head and tail atoms, etc). in the "examples" page of the antechamber
web site (which in turn you reach from the Amber web site):
http://amber.scripps.edu/antechamber/pro4.html
....hope this helps....dac
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Received on Mon Oct 11 2004 - 17:53:01 PDT
