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 - 14:30:03 PDT
