Hi all,
I'm interested in creating some AMBER parameters for 4-hydroxylysine,
and I wondered if anyone had already done this? If so would they be
willing to share both the parameters and their method?
If noone has already done this, how does one go about creating
parameters for a residue, which will then be part of a peptide
sequence? I can create parameters using GAFF for a complete small
molecule, but the residue I need should contain unterminated groups, in
the same way that the residues already included in AMBERTOOLS are, for
example in all_amino94.in? Could anyone tell me how the residue
parameters were generated in the first place in those files? Is that
documented anywhere?
One method, which I have already tried, was to create parameters for
4-hydroxylysine with terminating groups using GAFF and GAMESS to
estimate the charges. I hoped to modify the prep file manually to create
a one for the 4-hydroxylysine residue. But I wasn't sure how to do that
properly!
Another method was to make the tri-peptide NLYZ-LYZ-CLYZ as a single
molecule and some how extract the appropriate information. But again, I
wasn't sure what I needed to keep/throw away and if that would be a
valid approach?
Any advice/pointers in these matters would be greatly appreciated.
I expect I'm missing something blindingly obvious!
Thanks!
Chris
--
Dr Chris Forman
Department of Chemistry
University of Cambridge
+44(0) 1223 336471
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Received on Tue Aug 27 2013 - 08:30:07 PDT
