[gmx-users] help and a tutorial

[Tsjerk Wassenaar]

Hi Sebastien,

You shouldn't have used the -missing option. This leaves the atom out,
leaving you with a broken leucine. Apparently the pdb file has missing
atoms. Before setting up a simulation from a pdb file, first look for
missing atoms and residues and fix these if present (or actually, if not
present ;)). The SwissPDB Viewer will conveniently add missing atoms upon
loading a pdb file. Missing residues will require a bit more effort.

The CA-CA2+ warning is ok, if these should be CA2+ that is. The occupancy
unequal to one warning notifies you that some residues are present in
different configurations. This is also not a problem. In terms of MD it may
be good to take both configurations as starting points.

Good luck!

Tsjerk
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