Thanks a lot, Jason. This is essentially what I found, since I was loading
in a PDB file, but I didn't put it together quite like that since I've
never had to use Leap's "sequence" command.
Have a great night, and thanks again,,
Kamali
On Sun, Jun 17, 2012 at 4:59 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Sometimes you need to add C and N to terminal amino acids and sometimes you
> don't.
>
> If you are loading a protein PDB (or nucleic acid PDB or some standard
> biological polymer), 'terminal' residues are automatically detected.
> Therefore, you *never* have to add C/N to residues in a conforming PDB
> (that is, a PDB that conforms to the PDB standard for proteins/nucleic
> acids).
>
> Separate peptide chains defined in a PDB, as in a non-bonded dimer, will
> appropriately have multiple terminal residues inserted. The residue
> directly before a TER card will be a C-terminus, and one directly after a
> TER card will be the N-terminus of the next peptide chain.
>
> If you are using the "sequence" command, or some other command where you're
> using tleap to build the sequence, THEN you need to use the C/N-terminal
> names.
>
> For example:
>
> mol = sequence {NALA ALA CALA}
>
> will produce the proper charged, trialanine peptide chain. The command:
>
> mol = sequence {ALA ALA ALA}
>
> will produce a trialanine with incomplete valences.
>
> HTH,
> Jason
>
> On Sun, Jun 17, 2012 at 3:51 PM, Kamali Sripathi <ksripath.umich.edu>
> wrote:
>
> > Dear Amber Users,
> >
> > I'm trying to prepare a protein pdb file with AmberTools1.4, in
> preparation
> > for equilibration and production run with Amber10/11. When I tried to
> > insert C's and N's in the names of the C- and N-terminal residues (e.g.,
> > ALA --> CALA), Leap "created a new residue with the name CAL", which
> > indicates to me that the C isn't necessary. I had been leaving the
> residues
> > as standard; however the Ambertools manual tells me that leaving the
> > residues as standard means that they will have incomplete valences. I
> > didn't see this when I visualized my protein in PyMol (i.e., the
> N-terminal
> > residues had NH3 groups, and the C-terminal groups had COO groups).
> > However, before continuing I just wanted to make sure what is best
> > practice.
> >
> > Please let me know if there are previous mailing list threads or other
> > sources that address my question. Otherwise, any thoughts or comments
> would
> > be greatly appreciated!
> >
> > Thank you,
> >
> > Kamali Sripathi
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Sun Jun 17 2012 - 17:00:02 PDT
