Re: [AMBER] Generating topology files for non standard amino acid residue

From: Jason Swails <jason.swails.gmail.com>
Date: Sun, 12 Feb 2012 22:40:31 -0500

What do you mean "recognized as an amino acid"? There are very few situations in the amber programs that actually make use of that distinction.

Also, if it's a modified amino acid I don't know that gaff is the best force field to be using to parametrize it. Does FF10 not have the appropriate parameters? Has anyone else parametrized that residue yet? (RED Database is a good place to look, as is the Bryce parameter website that is easily found googling bryce and amber).

In any case, you should run some short dynamics on some test systems with your amino acid residue (maybe sandwiched between a couple alanines or something) and just make sure that some of the properties you can measure make physical sense (like phi-psi distributions, etc), just to be sure that nothing is drastically wrong.

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On 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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Received on Sun Feb 12 2012 - 20:00:02 PST