The only use leap makes of bond orders is for minimizing in xleap.
Since this isn't used by anyone I know of, it's not a big deal.
Note that the bond order doesn't play a part in the force field.
Bill
David A Case <case.biomaps.rutgers.edu> wrote:
> On Thu, Mar 07, 2013, Marko Wehle wrote:
> >
>
> > additionally I have to mention, a similar problem exists for tleap
> > reading mol2 files, it ignores the flags for bonds and makes a single
> > bond out of a double bond for example.
>
> This is not a (real) problem: Amber makes no use of bond orders (which is why
> the output mol2 doesn't get them right either.) Be sure that you need to have
> the correct bond orders in whatever program you are building the mol2 file
> for.
>
> (Nevertheless, we should try to fix the output, at least, since other programs
> may expect bond orders to be correct).
>
> ...dac
>
>
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Received on Thu Mar 07 2013 - 16:00:03 PST
