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
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Jun 17 2012 - 14:00:01 PDT
