Hi David,
Many thanks for these pointers. I was able to use this information and
now have suitable parameters for Hydroxylysine.
Gamess outputs a charge file which appeared to be in the same format as
the .crg file in the hydroxyproline example, so I could leap to step 5,
and then step six as you suggested.
Just a question of knowing about and then using prepGen properly and how
to define the residue using the mainchain terminology.
Many thanks.
Chris
On 27/08/2013 17:11, David A Case wrote:
> On Tue, Aug 27, 2013, Chris Forman wrote:
>> 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,
> Detailed instructions for antechamber are here:
>
> http://ambermd.org/antechamber/pro4.html
>
> Since you already have charges, you only need to do step 6: in short, create a
> "mainchain" file, then feed that, plus the .ac, .prepi or .mol2 file for the
> capped model compound, to the prepgen program.
>
> Unfortunately, this information somehow never made it into the AmberTools
> manual. [Developers: (a) the prepgen part of the manual should be expanded;
> (b) the page above should, simplified and updated, should be made into a
> tutorial.]
>
> ....hope this helps...dac
>
>
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Received on Thu Aug 29 2013 - 06:00:03 PDT
