prepare task


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Hi,

I try to use qmmm task (for example dynamics). For this task need .rst and .top files, generated by prepere task. There is a question: how to create correctly pdb from xyz or cml files?

Example xyz-files
Example nw-files

If use for creating pdb files, openbabel, prepare task:

1 geom_rtdb_load: "geometry" -> "geometry"
 ------------------------------------------------------------------------
 cons_init: no geometry        72
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
  current input line : 
    33: task prepare
 ------------------------------------------------------------------------


or missing atoms.

Clicked A Few Times
Look for information on pdb format at http://www.wwpdb.org/docs.html
and see this


http://nwchemgit.github.io/index.php/QMMM_Appendix#Preparing_QM.2FMM_calculations_from_scrat...


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