Transition state

From: Luca Bellucci (
Date: Thu Sep 21 2006 - 03:45:49 CDT

Hi All,
When I parametrize a transition state in charmm potential, there are atom and
link not usual. In particular I would want to parametrize Transition state
like SN2, but I do not know how make not standard bond. For example, how
make oxygen with 3 bond, therefore 2 streching and angle. At this moment I
know only "PATCH CHARMM" method ,
but I have some problem like this:

1- Autopsf add arbitrary atom.....but I can resolve with psfgen and PATCH ...
  FATAL ERROR: Atom 1293 has bad group size. Check for duplicate bonds.
where atom 1293 is oxygen of TS.

Thanks in advance for any Help

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