modified on 6 February 2014 at 16:41 ••• 2,617 views

Release64:Qmmm rename

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This directive is allows to rename atoms in the QM region, based on the external file which specifies desired name( (1st column) and its PDB index (2nd column). The file is assumed to be located in the current run directory.
This directive is allows to rename atoms in the QM region, based on the external file which specifies desired name( (1st column) and its PDB index (2nd column). The file is assumed to be located in the current run directory.
 +
 +
For example, if we need to rename atoms CB and OG that are part of our QM region
 +
 +
  ...
 +
  ATOM    13  N  SER    2      0.211  0.284  -1.377        0.00    N
 +
  ATOM    14  H  SER    2      0.886  1.158  -1.257        0.00    H
 +
  ATOM    15  CA  SER    2      -0.320  -0.351  -0.166        0.00    C
 +
  ATOM    16  HA  SER    2      -1.405  -0.183  -0.132        0.00    H
 +
  ATOM    17  CB  SER    2      -0.001  -1.879  -0.106        0.00    C
 +
  ATOM    18 2HB  SER    2      1.092  -2.012  -0.038        0.00    H
 +
  ATOM    19 3HB  SER    2      -0.469  -2.317  0.784        0.00    H
 +
  ATOM    20  OG  SER    2      -0.452  -2.678  -1.192        0.00    O
 +
  ATOM    21  HG  SER    2      -1.351  -2.421  -1.392        0.00    H
 +
  ATOM    22  C  SER    2      0.252  0.338  1.076        0.00    C
 +
  ...
 +
 +
the following amm block can be used
 +
  ...
 +
  qmmm
 +
  ...
 +
  rename name.dat
 +
  ...
 +
  end
 +
 
 +
  task qmmm dft energy
 +
 +
 +
where name.dat file
 +
 +
C1 17
 +
OX 20
 +
 +
Here atoms are identified by the corresponding PDB atom index and renamed from default element based naming to C1 and OX.

Revision as of 16:32, 6 February 2014

rename <filename>

This directive is allows to rename atoms in the QM region, based on the external file which specifies desired name( (1st column) and its PDB index (2nd column). The file is assumed to be located in the current run directory.

For example, if we need to rename atoms CB and OG that are part of our QM region

 ...
 ATOM     13  N   SER     2       0.211   0.284  -1.377        0.00     N
 ATOM     14  H   SER     2       0.886   1.158  -1.257        0.00     H
 ATOM     15  CA  SER     2      -0.320  -0.351  -0.166        0.00     C
 ATOM     16  HA  SER     2      -1.405  -0.183  -0.132        0.00     H
 ATOM     17  CB  SER     2      -0.001  -1.879  -0.106        0.00     C
 ATOM     18 2HB  SER     2       1.092  -2.012  -0.038        0.00     H
 ATOM     19 3HB  SER     2      -0.469  -2.317   0.784        0.00     H
 ATOM     20  OG  SER     2      -0.452  -2.678  -1.192        0.00     O
 ATOM     21  HG  SER     2      -1.351  -2.421  -1.392        0.00     H
 ATOM     22  C   SER     2       0.252   0.338   1.076        0.00     C
 ...

the following amm block can be used

 ...
 qmmm
  ...
  rename name.dat
  ...
 end
 
 task qmmm dft energy


where name.dat file

C1 17
OX 20

Here atoms are identified by the corresponding PDB atom index and renamed from default element based naming to C1 and OX.