I recommend using the RED server (
http://q4md-forcefieldtools.org/REDS/).
~Aron
On Sun, Feb 12, 2012 at 9:41 PM, Matthew D Antalek
<mantale1.binghamton.edu>wrote:
> Hi all,
>
>
> I am having a bit of trouble with getting AMBER to recognize the
> topology file for a non standard amino acid residue I have created. I was
> able to create the parameter-topology file (.prmtop) but I do not
> understand how to create some other files so that the system can recognize
> the residue as an amino acid residue. I have tried to work with this
> tutorial : http://ambermd.org/antechamber/pro4.html but I do not have
> access to gaussian. I was able to generate the parameters for the molecule
> using GAFF, so if anyone knows how to get the system to register the
> molecule as an amino acid that would be great.
>
> Thanks,
> Matt
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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Sun Feb 12 2012 - 19:30:02 PST
