[gmx-users] dummy atoms
David van der Spoel
spoel at xray.bmc.uu.se
Tue Oct 22 22:05:49 CEST 2002
On Wed, 2002-10-23 at 11:08, Frank Wennmohs wrote:
> Hello all!
> Is it possible that there are some restrictions
> as to where dummy atoms can be placed in
> a molecule's topology?
> As I performed the following scenario:
> I inserted dummy atoms in a protein topology generated
> by pdb2gmx and renumbered all atoms and charge groups thereafter.
> Afterwards gmx complained about not defined angles like
> simple backbone angles!
> Has anyone an explanation for this?
DId you also renumber all the angles and bonds etc.?
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Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 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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