Dear Chris,
See R.E.D. (perl version) & R.E.D. Server at q4md-forcefieldtools.
And in particular see the tutorials:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
vs
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
where all the fragments are automatically generated from a single
dipeptide molecule.
Atom types are not added in the FF lib generated by R.E.D. perl and
have to be added using a LEaP script (see examples in R.E.DD.B.).
R.E.D. Python, which will be released through R.E.D. Server Dev. next
September does perform atom typing (and far more).
regards, Francois
> 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!
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Received on Thu Aug 29 2013 - 02:00:03 PDT
