Hi Matt,
You can for sure make a library. What you will get from the RED Server is
a .mol2 file that you can load into LeAP. It will have all the bonds and
the partial charges, then you will just tell it what kind of atoms each one
is (CT for a sp3 hybridized carbon, or whatever AMBER uses, this part
should be extremely straight forward since most of your residue will have
the same atom types as tyrosine, and you can look at lists of atom types to
get the extra one), then you can just "saveoff" in LeAP to make a library.
In terms of using the RED Server: you could do something like you are
saying, perhaps just make your non-standard residue with ACE and NME caps
and then set it such that the net charge of your residue in the middle is
0. But, a far better option is to just make a dipeptide of your residue,
so two of your modified tyrosines next to each other, one with a COO-
terminus and one with an NH3+ terminus. The RED Server can take that and
automatically generate for you the .mol2 files for a C-terminal modified
residue, N-terminal modified residue, and the case where the residue is in
the middle of a protein somewhere. This way you can make all three
libraries such that you can handle mutations to your non-standard residue
at any site.
~Aron
On Tue, Feb 14, 2012 at 2:44 PM, Matthew D Antalek
<mantale1.binghamton.edu>wrote:
> 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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> > > 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Tue Feb 14 2012 - 19:30:03 PST
