From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Nov 19 2010 - 21:50:10 CST
The problem is actually in the parameter file, and is just a bad
interaction of NAMD's logic for dealing with lone pairs with the setup
there. NAMD requires there to be a bond between the lone pair and oxygen
to recognize where the lone pairs are, but before reaching that point it
discards all bonds with zero force constants. Setting the LP-OT bond to
have a nonzero force constant should fix things (I suggest a large
value, since namd does not enforce the constraints on the TIP4 geometry
Please let me know if you have any more questions.
On 11/19/2010 01:02 PM, Jeffery Klauda wrote:
> I made the XPLOR psf in charmm with the two topology files attached.
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