SET word real
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.