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QMMM Restart and Topology Files

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QM region definition

Contents

Restart and topology files

The structure of the system in QM/MM calculations is provided by the restart file (extension .rst) and not by the geometry block as it would be for pure QM calculations. The parameters of classical interaction are given by the topology file (extension .top). These two files are REQUIRED for QM/MM calculations and can be generated by the prepare module. In a typical setting this "preparation stage" is performed separately from the main QM/MM simulation.

Prerequisites

The necessary prerequisites for the preparation of topology and restart files for QM/MM simulations are:

  • Properly formatted PDB file for the system.
  • Fragment Files (extension .frg)
  • Parameter Files (extension .par)

A number of fragment files as well as standard Amber type force parameter files are provided with the NWChem distribution. However, user should be prepared to generate additional fragment and parameter files for nonstandard cases.

QM region definition


QM/MM Restart and Topology files: Prerequisites | QM region definition | Solvation | Permanent Constraints



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.

Solvation


QM/MM Restart and Topology files: Prerequisites | QM region definition | Solvation | Permanent Constraints



During the preparation stage of QM/MM calculations the system may also be solvated using solvate directive of the prepare module. It is recommended that solvation is performed in conjunction with center and orient directives.

Here is an example where the ethanol molecule is declared quantum and solvated in a box of spce waters:

title "Prepare QM/MM calculation of solvated ethanol"
start etl
prepare
source etl0.pdb
new_top new_seq
new_rst
#center and orient prior to solvation
center
orient
#solvation in 1 nm by 2 nm by 3 nm box
solvate box 1.0 2.0 3.0
#the whole ethanol is declared quantum now 
modify segment 1 quantum
update lists
ignore
write etl_ref.rst
write etl_ref.pdb
end
task prepare

Permanent Constraints


QM/MM Restart and Topology files: Prerequisites | QM region definition | Solvation | Permanent Constraints



Fixing atoms outside a certain distance from the QM region can also be accomplished using prepare module. These constraints will then be permanently embedded in the resulting restart file, which may be advantageous for certain types of QM/MM simulations. The actual format for the constraint directive to fix whole residues is

fix segments beyond  <real radius>  <integer residue number>:<string atom name>

or to fix on atom basis

fix atoms beyond  <real radius>  <integer residue number>:<string atom name>

This example illustrates the use of permanent fix directives during preparation stage

start etl 
prepare
source etl0.pdb
new_top new_seq
new_rst
center
orient
#solvation in 40 A cubic box
solvate cube 4.0
modify segment 1 quantum
#fix residues more than 20 A away from ethanol oxygen atom
fix segments beyond 2.0 1:_O
update lists
ignore
write etl_ref.rst
write etl_ref.pdb
end
task prepare