Thanks Francois,
I was able to achieve my objective using ambertools prepgen program.
Once I had access to the right instructions!
Will check out R.E.D and learn more about it.
Many thanks
Chris
On 29/08/2013 09:47, FyD wrote:
> 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 - 06:00:03 PDT
