Minimization messes up C terminal

From: Pavan G (pavan.namd_at_gmail.com)
Date: Wed Jun 16 2010 - 10:32:42 CDT

Hello All,
I am trying to run a NAMD simulation of a protein in water with Charmm27 ff.
The terminal carboxyl carbon and two oxygens look fine in the starting
structure but as soon as the minimization starts the two oxygens come close
to each other and the simulation fails later when I start NVT and/or heat
beyond 250K. The charges on the oxygens are -0.67 each and charge on
carboxyl carbon is 0.34 as expected. I fail to see why minimization would
force two highly (both negative) charged atoms close to each other. Any help
would be appreciated. The C terminal residue was created with the cter patch
in Charmm.
Thanks,
Pavan

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