To use the L template, you would have to come up with the desired
config in pdb (all residues).
If you make one residue in pdb, you could use it to define
an alternate template file (see tutorials for adding a new
residue type, noting that atom types and charges could come
from the TYR template), load that, then use sequence
in leap to make a strand. If you load the general residue
templates, I would avoid a name collision by using a different
residue name in this case.
So whatever is easier.
> true - if I want to generate a polymer with how can I use with for an
> example sequence in leap? Or is there another way for creating the polymer
> from a single pdb file of the residue type ?
> On Tue, Jul 20, 2010 at 10:12 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > Please excuse my lack of chemistry, but is the D-isomer
> > chemically different from the L? If they are chemically
> > the same, all you should need is to load a pdb with the
> > D-isomer - as long as atoms are not missing for the template
> > to supply from its L form, things would be ok in that simulations
> > could be run. In this case, the only reason for developing
> > an L-isomer template would be to have different atomic
> > charges if L is not a mirror of D, or for convenience in
> > placing missing atoms.
> >
> > Bill
> >
> > > You will have to build it first, though you can name all of the residues
> > > TYR. The templates loaded into leap are only for the one form.
> >
> > > Good luck!
> > > Jason
> >
> > > On Tue, Jul 20, 2010 at 12:52 PM, Jorgen Simonsen <jorgen589.gmail.com
> > >wrote:
> >
> > > > Hi all,
> > > >
> > > > I am simulating a L-Tyr-L-Tyr-L-Tyr-L-Tyr-LTyr ect peptide and want to
> > > > observe if the same is true for the D-isomer. I use the sequence
> > function
> > > > within ambertools to generate the peptide
> > > >
> > > > seq = sequence { TYR TYR TYR TYR TYR}
> > > >
> > > > is it possible to do the same with the D-isomer or do I have to build
> > it
> > > > first? Or is it already available ?
> >
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Received on Tue Jul 20 2010 - 15:00:03 PDT
