need help to prepare my first QM/MM input
yueyan... at gmail.com
Thu Jul 19 00:39:49 CEST 2012
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:
ABC 78.996 78.996 78.996
ALPHA_BETA_GAMMA 109.471 109.471 109.471
In addition, should I use 'KIND FE' or 'KIND Fe'? Is there any other basis
available for this metal besides 'DZVP-MOLOPT-SR-GTH'?
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