On Wed, May 12, 2004, Carsten Detering wrote:
>
> how do I proceed if I want to open a ring for thermodynamic integration? I
> have an isoindole ring, and I would like to make a C in the 5-ring an H, and
> bind this H to the atom next to it. How can I tell sander to bind the
> resulting H to one side, and remove the bond to the other? In smiles it
> would look something like [nH]1cc2ccccc2c1 -> NC=C1=CC=CC=C1.
>
You don't have to do anything special for rings in thermodynamic integration.
I am not sure from your description what the product is supposed to be. [The
five membered ring would have a CH group that would need to be mutated
somehow, not just a C, and I am not quite sure what you mean by "the atom
next to it" (is this the nitrogen, or is it a carbon in the 6-member ring?)
If you change the C to an H, you also have to do something with the H that was
originally bonded to this C.] But if you can't get going, it's probably best
to be more clear about what the chemical stucture of the perturbed state
is to be.
....maybe this will help you get going...dac
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed May 12 2004 - 20:53:01 PDT
