Transition state

From: Luca Bellucci (bellucci14_at_unisi.it)
Date: Thu Sep 21 2006 - 03:45:49 CDT

• Next message: Alessandro Cembran: "Re: Hexagonal boundary conditions"
• Previous message: Vani Krishna: "NAMD installation on Cray XD1 (AMD opteron 64-bit)"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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 ...
2-NAMD
  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
Luca
 

• Next message: Alessandro Cembran: "Re: Hexagonal boundary conditions"
• Previous message: Vani Krishna: "NAMD installation on Cray XD1 (AMD opteron 64-bit)"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:01 CST