Re: Minimization messes up C terminal

From: Peter Freddolino (
Date: Wed Jun 16 2010 - 11:48:05 CDT

Hi Pavan,
this usually happens if you use a CMAP topology file but do not
regenerate angles and dihedrals after psf generation. It would help if
you could post the name of the topology file that you're using, and the
version of vmd.

On 06/16/2010 11:32 AM, Pavan G wrote:
> 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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