Just as another tidbit of information, the RED server has a tutorial for
this kind of thing. The problem you are likely coming across, in which you
say it is not recognized as an amino acid, is that it doesn't have connect
information. You need to add a connect0 and connect1, probably also a head
and tail definition. such that it knows your molecule is not a stand-alone
molecule, but intended to be used as a fragment. This information tell
LeAP which atoms in your residue are meant to connect to other residues
when they are a chain. Again I recommend the RED server and associated
tutorial, they have a special option on their server for making
non-standard amino aicds.
~Aron
On Sun, Feb 12, 2012 at 10:40 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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>
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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 - 20:00:02 PST
