I wouldn't use antechamber to make a non-standard residue, but maybe that's
just me.
when you edit your residue in leap does it look ok? That is, are all the
bonds actually present that you wanted?
I have no idea about this OMIT_NAME.
I suggest making a dipeptide of your residue. Load the structure in leap,
edit it and add all the bonds manually. Edit the charges and enter
something reasonable/similar to what you got using Antechamber, then relax
the structure. Then save that as a pdb. Submit that to the RED Server
using their automated non-standard residue generating option. You are
done. At least that is what I would do.
~Aron
On Mon, Feb 13, 2012 at 11:55 PM, Matthew D Antalek <mantale1.binghamton.edu
> wrote:
> Dear all,
>
> I was able to get through most of the tutorial
> http://ambermd.org/antechamber/pro4.htm<
> http://ambermd.org/antechamber/pro4.html>
> without
> any problems except for then end. When I created the prepi file, I got this
> message:
>
>
> Info: there is a bond linking a non-head and non-tail residue atom (C1) and
> an omitted atom (H3).
> You need to specifically add this bond in leap using the command
> 'bond <atom1> <atom2> [order]'
> to link C1 to an atom in another residue (similar to disulfide bonds)!
>
> Info: there is a bond linking a non-head and non-tail residue atom (C1) and
> an omitted atom (C3).
> You need to specifically add this bond in leap using the command
> 'bond <atom1> <atom2> [order]'
> to link C1 to an atom in another residue (similar to disulfide bonds)!
>
> I am not sure exactly what I should do to correct this ( or if I even need
> to ). I basically copied what the tutorial did, naming all the atoms
> besides the 3 mainchain atoms as OMIT_NAME. Also, when did a quick check of
> the structure in xleap (creating a polypeptide NALA 3FY CALA), I was able
> to create a sequence using the new amino acid, but it seems that all the
> atoms I listed as OMIT_NAME atoms are not displaying.
>
> Thanks,
> Matt
>
>
> On Sun, Feb 12, 2012 at 11:00 PM, Matthew D Antalek <
> mantale1.binghamton.edu
> > wrote:
>
> > 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
> >>
> >
> >
>
> _______________________________________________
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>
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Tue Feb 14 2012 - 06:00:02 PST
