[gmx-users] terminal residues come off and fragment

[Chris Gaughan]

David,

No I did not use vitual sites. 

--- David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> On Wed, 2005-09-07 at 14:51 -0700, Chris Gaughan
> wrote:
> > Hello all,
> > 
> > I'm simulating the dimerization of two alpha
> helices.
> > I ran the energy minimization in vacuo and looked
> at
> > the resulting coordinate file (.gro) in PyMol. The
> > result looks very close to what I expected,
> however,
> > there seem to be asterisks where the peptides
> overlap
> > and pieces of the terminal residues seem to
> > have.....fragmented (there are pieces of them
> between
> > the two peptides).
> did you use virtual sites (dummies)?
> > 
> > Can someone explain this?
> > 
> > Thanks
> > Chris
> > 
> > 
> > 
> > 
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> -- 
> David.
>
________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular
> Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala
> University.
> Husargatan 3, Box 596,          75124 Uppsala,
> Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org  
> http://xray.bmc.uu.se/~spoel
>
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