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.

  • Marat Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Look for information on pdb format at http://www.wwpdb.org/docs.html
and see this


http://www.nwchem-sw.org/index.php/QMMM_Appendix#Preparing_QM.2FMM_calculations_from_scrat...
Edited On 2:19:05 PM PST - Tue, Nov 29th 2011 by Marat


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