On Tue, Aug 17, 2010, Marek Maly wrote:
>
> I want to simulate bilirubin (
> http://upload.wikimedia.org/wikipedia/commons/6/6a/Bilirubin.svg ) which
> contains double bonds.
> Shall I take care in this case about the double bons during Atechamber
> parametrisation (creation of prepin, frcmod files )
> or later in tleap/sleap after loading the structure or it is enough to
> provide just reasonable structures
> in PDB format and Antechamber or later tleap/sleap will do automatically
> proper atom types assignment/double bonds recognition ?
Amber and GAFF force fields don't have any formal concept of bond order.
A typical input to antechamber would be a pdb file, which just has
coordinates. You do need to take care with conjugated systems, however --
these are tough for simple force fields, and you may not be fully happy with
what the automated procedures produce.
....dac
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Received on Tue Aug 17 2010 - 15:30:03 PDT
