Qmmm preparation basic
One of major required pieces of information that has to be provided in the prepare block for QM/MM simulations is the definition of the QM region. This can be accomplished using modify directive used either per atom
modify atom <integer isgm>:<string atomname> quantum
or per segment/residue basis
modify segment <integer isgm> quantum
Here isgm and atomname refer to the residue number and atom name record as given in the PDB file. It is important to note that that the leading blanks in atom name record should be indicated with underscores. Per PDB format guidelines the atom name record starts at column 13. If, for example, the atom name record "OW" starts in the 14th column in PDB file, it will appear as "_OW" in the modify atom directive in the prepare block.
In the current implementation only solute atoms can be declared as quantum. If part of the solvent has to be treated quantum mechanically then it has to redeclared to be solute. The definition of QM region should be accompanied by update lists and ignore directives. Here is an example input file that will generate QM/MM restart and topology files for the ethanol molecule:
title "Prepare QM/MM calculation of ethanol" start etl prepare #--name of the pdb file source etl0.pdb #--generate new topology and sequence file new_top new_seq #--generate new restart file new_rst #--define quantum region (note the use of underscore) modify atom 1:_C1 quantum modify atom 1:2H1 quantum modify atom 1:3H1 quantum modify atom 1:4H1 quantum update lists ignore #--save restart file write etl_ref.rst #--generate pdb file write etl_ref.pdb end task prepare
Running the input shown above will produce (among other things) the topology file (etl.top), the restart file (etl_ref.rst), and the pdb file (etl_ref.pdb). The prefix for the topology file follows after the rtdb name specified in the start directive in the input (i.e. "start etl"), while the names for the restart and pdb files were specified explicitly in the input file. In the absence of the explicit write statement for the restart file, it would be generated under the name "etl_md.rst". The pdb file would only be written in the presence of the explicit write statement.
Tip: It is strongly recommended to check the correctness of the generated pdb file versus the original "source" pdb file to catch possible errors in the formatting of the pdb and fragment files.