change

Change specified parts of a topology.

change [parm <name> | parmindex <#> | <#> | crdset <COORDS set> ] { resname from <mask> to <value> | chainid of <mask> to <value> | oresnums of <mask> min <range min> max <range max> | icodes of <mask> min <char min> max <char max> resnum <#> | atomname from <mask> to <value> | addbond <mask1> <mask2> [req <length> <rk> <force constant>] removebonds <mask1> [<mask2>] [out <file>] }

parm <name> | parmindex <#> | <#> | crdset <COORDS set> Topology to change.
resname from <mask> to <value> Change residue names for residues in <mask> to the given <value>.
chainid of <mask> to <value> Change the chain ID of residues in <mask> to given <value>.
oresnums of <mask> min <range min> max <range max> Change original residue numbers (to e.g. original PDB numbers) of residues in <mask> to a range starting from <min> and ending with <max>.
icode of <mask> min <char min> max <char max> <resnum> <#> Change residue insertion codes of residues in <mask> to a range of characters starting from <min> and ending with <max>; set the original residue number to <resnum>.
atomname from <mask> to <value> Change atom names for atoms in <mask> to the given <value>.
addbond <mask1> <mask2> Add bond between atom specified by <mask1> and atom specified by <mask2>.
[req <length>] The equilibrium bond length in Angstroms.
[rk <force constant>] The bond force constant in kcal/mol*Angstrom.
removebonds <mask1> [<mask2>] Remove bonds from atoms in <mask1>. If <mask2> also given, remove bonds between atoms in <mask1> and atoms in <mask2>.
[out <le>] If specified, write removed bonds to <file> with format ‘<residue name> <residue num> <atom name> <atom num>’.

Change specified parts of the specified topology. For example, to change atoms named ‘HN’ to ‘H’ in topology 0:

change parmindex 0 atomname from @HN to H