Aron,
No, the only atoms that I can see in leap are the head and tail atoms
and the mainchain atoms; all the atoms that I labeled as OMIT_NAME in the
mainchain.3fY file are not present (and subsequently the bods as well). My
question about using the RED server to generate topologies of non-standard
residues is would I be able to make a library for the residue, or would I
have to resubmit structures every time I need to use it? Also, when you say
a dipeptide of the residue, do you mean that one residue is the
non-standard amino acid that I want to create (in my case I am making 3
formyl tyrosine) and then use a dummy residue like alanine, or do I make a
dipeptide consisting of two 3-formyl-tyrosine residues?
Thanks,
Matt
On Tue, Feb 14, 2012 at 8:43 AM, Aron Broom <broomsday.gmail.com> wrote:
> 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 - 12:00:03 PST
