[gmx-users] help and a tutorial

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Oct 16 10:46:44 CEST 2005

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!

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20051016/7aa240a4/attachment.html>

More information about the gromacs.org_gmx-users mailing list