On Thu, 2014-03-27 at 16:50 +0200, Fabian Glaser wrote:
> OK thanks!
>
> One more thing, how can I check that the double / single bonds after antechamber finishes are correct?
Amber has no concept of "double" and "single" bonds. You should check
the atom types instead. Atoms typically involved in double bonds are
assigned a specific type (typically described as "sp2" for carbon, for
instance). Types are used to differentiate between atoms that are the
same element but have different 'properties' (like carbons attached to
oxygen, carbons in an aromatic ring, carbons in a ketone group, etc.).
In force field language, a "double bond" is simply a shorter, stiffer
spring, and these are assigned based on atom types.
The force field files themselves ($AMBERHOME/dat/leap/parm/gaff.dat, for
instance) define and describe each atom type.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Mar 27 2014 - 08:30:04 PDT
