Dear Albert,
> I found that there is no bond order information from the output of
> RED .mol2 file. To be sure the bond order information is correct before
> running acype, I am wondering how can we add bond order information by
> ourselves to the .mol2 file?
R.E.D. does not generate bond order information...
Indeed, a simple, double or a triple bond does not exist in an
empirical force field. In the Hooke's law
(
http://en.wikipedia.org/wiki/Hooke's_law) a bond is represented by
its equilibrium value and a force field constant; the later is
'simply' different for a simple, double or a triple bond... Thus,
there is no need to define a bond order in this particular case
(Antechamber defines a bond order for some internal reasons (atom
typing?) and the choice has been been made to print it; I guess).
regards, Francois
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Received on Wed Jun 13 2012 - 01:00:03 PDT
