[gmx-users] terminal residues come off and fragment

[David van der Spoel]

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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