[gmx-users] help and a tutorial

Sebastien Gerega seb at gerega.net
Sun Oct 16 12:28:45 CEST 2005

Are there any other programs to do this kind of thing? I have tried 
using Swiss-PDBViewer and am really having difficulties with it. Doesn't 
seem to run well on my system and when I try and save my changes as a 
PDB file it seems to happen ok but then when I go and look for the file 
it was not created...

Tsjerk Wassenaar wrote:

> 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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