tleap does not use bond order for much, if anything. As a result, there is
little incentive to save bond orders and propagate those.
Here is a previous discussion of the topic taken from googling "tleap mol2
bond order":
http://archive.ambermd.org/201302/0352.html
While there is a variable inside tleap for reading bond orders, it is not
used reliably (due to its unimportance in force field parametrization
inside tleap). Therefore, I suspect the mol2 reader and writer ignored
bond orders and set them all to 1. In this case, there is nothing you can
do short of fixing the code. (Again, because it's unimportant for the most
part, it won't be high on anybody's list of things-to-do.)
If you are doing something where this number is important, you're probably
better off using another program whose focus is more in line with what you
are doing.
HTH,
Jason
On Thu, Mar 7, 2013 at 1:44 PM, Marko Wehle <Marko.Wehle.mpikg.mpg.de>wrote:
>
> Hello AMBER users,
> 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.
>
> Cheers
> Marko
>
>
> -----Ursprüngliche Nachricht-----
> Von:
> Gesendet: Do 07.03.2013 18:08
> An: amber.ambermd.org
> Betreff: tleap output of mol2 format with incorrect bond order
>
>
> Hey and hello AMBER users and Developers,
> today I had the experience that by modelling in tleap the output of the
> mol2 format lacks an information.
> In my experience it is the correct bond order, if I set a bond order to
> "D" and write a mol2 file, it puts a "1" instead of a "2".
> But internally tleap sets it correct, by writing an off file as lib with
> the same content, the bond order is correctly set to "2".
>
> Is there a fix for that?
>
> Many thanks for your help.
> Cheers
> Marko
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 07 2013 - 12:30:02 PST
