Dear Professor Case,
Thank you. My apologies for lacking clarity. Your guess is correct, I am
modifying the side chain of a non-terminal lysine. I know to examine the N
(original LYS) - C (ACE) bond, but what other bonds should I examine?
Furthermore, my understanding is to examine these bonds in the prmtop file,
but my level of expertise in reading prmtop files is not where it should
be. Could you point me in the direction of a resource for this?
Thanks for your prompt and thoughtful response,
David Winogradoff
~~~~~~~~~~~~~~~~~~~~~
Research Assistant
Chemical Physics
University of Maryland
College Park
~~~~~~~~~~~~~~~~~~~~~
On Mon, Feb 10, 2014 at 10:00 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Feb 10, 2014, David Winogradoff wrote:
> >
> > I am acetylating a lysine in my PDB using xLeap by adding an "ACE."
>
> This is not very clear (at least to me). Assuming you are modifying the
> side
> chain of a non-terminal lysine, please examine the bonds around the
> acetylation site carefully to make sure you have what you want.
>
> > Marking per-residue atom chain types.
> > (Residues lacking connect0/connect1 -
> > these don't have chain types marked:
> >
> > res total affected
> >
> > ACE 1
> > CGLN 1
> > NSER 1
> > )
> > (no restraints).
>
> Above looks fine...the messages are for information, and are not errors.
>
> ...dac
>
>
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Received on Mon Feb 10 2014 - 20:00:02 PST
