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 Tue Aug 27 2013 - 09:30:03 PDT
