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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Received on Sun Jun 17 2012 - 13:00:02 PDT
