Dear prof. Case,
thank you for your prompt and clear answer !
Best wishes,
Marek
Dne Wed, 18 Aug 2010 00:18:00 +0200 case <case.biomaps.rutgers.edu>
napsal/-a:
> 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 Wed Aug 18 2010 - 05:30:03 PDT
