3.1.5.5 RTF Set Command

Syntax

     SET word real

Function

When residues in the topology file are patched when a segment is made from them, some atomic charges must be adjusted. Currently, the program calculates the correct charges for the explicit hydrogen and extended atom topology files, see Residue Topology Files. However, with other topology files, it does not.

The SET command provides a mechanism for assigning these charges in the topology file. The user specifies a variable name as the first operand in the command, and a charge value or adjustment in the second. These variable name, charge value pairs are stored with the topology file. If no variable name is available, then a default value is used which will give the correct values for the explicit hydrogen topology files.

The following table gives the currently used variables, default values, and their meaning.

     Variable       Default  Meaning
     
     CG_C3_PRIME     0.084   Charge increment for the 3' carbon in DNA.
     CG_C5_PRIME     0.092   Charge increment for the 5' carbon in DNA.
     CG_DISU_CB      0.022   Charge for the beta carbon in a disulphide
                             linkage.
     CG_DISU_SG     -0.032   Charge for the gamma sulfur in a disulphide
                             linkage.
     CG_FIRSTCA      0.020   Charge increment for the amino terminal alpha
                             carbon.
     CG_FIRSTN       0.710   Charge increment for the amino terminal
                             nitrogen in a protein.
     CG_LASTC        0.030   Charge increment for the carboxy terminal
                             carbonyl carbon.
     CG_LASTO       -0.200   Charge increment for the carboxy terminal
                             carbonyl oxygen.
     CG_O3_PRIME     0.163   Charge increment for the 3' oxygen in DNA.
     CG_O5_PRIME     0.147   Charge increment for the 5' oxygen in DNA.
     CG_PRO_FIRSTN   0.085   Charge of the amino nitrogen in an amino-
                             terminal proline. NOTE: the presence of this
                             variables signifies that prolines get special
                             treatment. If you omit it, then none of the
                             CG_PRO variables will have any effect.
     CG_PRO_FIRSTCD  0.079   Charge of the delta carbon in an amino-
                             terminal proline.
     CG_PRO_FIRSTCA  0.095   Charge of the alpha carbon in an amino-
                             terminal proline.
     CG_PRO_IHT1     0.225   Charge of the first amino terminal peptide
                             hydrogen in an amino-terminal proline.
     CG_PRO_IHT2     0.225   Charge of the second amino terminal peptide
                             hydrogen in an amino-terminal proline.

This particular mechanism used for charged should be viewed a temporary measure. There are plans to replace it with a more robust patching scheme.