SCM: QMMM

Usage of pdb2adf

The program works interactively. Given below in bold are the parts that the user has to type. In cases where the user agrees with the suggestion given by the program, the user can press the Enter key indicated with Enter.

 
                                  P D B 2 A D F - program   
                                     version 2005.01
                              Written by: Marcel Swart, 2005

                         This program uses AMBER parameter files
                            see: http://amber.scripps.edu



Do you want a logfile to be written (Y/n) ?

Enter

Please give name of PDB-file

hoh.pdb

 read fragments

Data Processed:
     Nat:          3
    Nmol:          1
 NChains:          0

Please wait, making connection tables
Now finding nearby atoms
Assigning chain ID to all residues
Completing residues for which only option is available

Refinding nearby atoms (including atoms added in residue completion)

 - - - - - - - - - - - - - - - - - - - - - - - - - - -
           Making Choices for Chain      0
 - - - - - - - - - - - - - - - - - - - - - - - - - - -

Completing residues with multiple options available, and solvent molecules

Checking positions of newly added atoms


Making choice for which molecules should be QM, which MM



Residues belonging to chain  0

Solvent molecules (SOL/HOH) belonging to this chain:
    1

Give the number of the molecule to be put in QM region (or 'c' to continue):

Putting HOH    1 in QM region

Give the number of the molecule to be put in QM region (or 'c' to continue):


Do you want to add solvent to your system (Y/n) ?

Enter



Solvent (box) available:
   1:  HOH     HOH  Water molecule
   2:  MOH     MOH  Methanol molecule
   3:  CHL     CHL  Chloroform molecule


Reading contents of solvent box p2abox.MOH                                                          
 
Box Shape options:
 1  Spherical box
 2  Cubic box
Make a choice:


Writing inputfile for chain   0

Using total charge   0.0 and total spin   0.0

Maximum atomic distance (Angs) from center        0.92
Give boxsize (def.:    15.00 Angs)

14.0

Using BOXSIZE value of  14.0000
Adding atoms for box     1  Added (Box):    84 (Total):    84  Excl. (1):   660  Excl. (2):     6
Adding atoms for box     2  Added (Box):   102 (Total):   186  Excl. (1):   642  Excl. (2):     6
Adding atoms for box     3  Added (Box):   102 (Total):   288  Excl. (1):   642  Excl. (2):     6
Adding atoms for box     4  Added (Box):   108 (Total):   396  Excl. (1):   642  Excl. (2):     0
Adding atoms for box     5  Added (Box):   120 (Total):   516  Excl. (1):   630  Excl. (2):     0
Adding atoms for box     6  Added (Box):    96 (Total):   612  Excl. (1):   654  Excl. (2):     0
Adding atoms for box     7  Added (Box):   108 (Total):   720  Excl. (1):   642  Excl. (2):     0
Adding atoms for box     8  Added (Box):   102 (Total):   822  Excl. (1):   642  Excl. (2):     6

Inputfile(s) written, everything processed, work has been done.
Thank you for using the PDB2ADF program.

================================
Normal ending of PDB2ADF program
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