Thanks, I did not know about the RED server before. I will try to go
through with the given tutorial and also look at the one on the RED server.
Thanks,
Matt
On Sun, Feb 12, 2012 at 10:50 PM, Aron Broom <broomsday.gmail.com> wrote:
> 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Feb 12 2012 - 20:30:01 PST
