need help to prepare my first QM/MM input

Yue yueyan... at gmail.com
Thu Jul 19 00:39:49 CEST 2012


Hello everyone,

I'm new to CP2K and I'm preparing a QM/MM input for a P450 enzyme complex 
with a heme (including iron) and a drug ligand. 

The MM equilibration has been done with AMBER so I'm stick with AMBER 
files, but after went through several threads here I found that AMBER files 
might not be easy to set up SHAKE constraint. I noticed someone mentioned 
fake run and then get PSF(?), can anyone give more details?

Also, I'm using an octahedral water box and I'm not sure if my &CELL 
setting in $SUBSYS section is correct:
    &CELL
      ABC 78.996 78.996 78.996
      ALPHA_BETA_GAMMA 109.471 109.471 109.471
    &END CELL

In addition, should I use 'KIND FE' or 'KIND Fe'? Is there any other basis 
available for this metal besides 'DZVP-MOLOPT-SR-GTH'? 

Thank you!

Regards,
Yue


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