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 <file>]
If specified, write removed bonds to <file> with format ‘<residue name> <residue num> <atom name> <atom num>
‘.
bondparm <mask1> [<mask2>] {setrk|scalerk|setreq|scalereq} <value>
Modify bond parameters in bonds selected by <mask1>
(and <mask2>
if specified) by specified <value>.
setrk
Set bond force constants to <value>
.
scalerk
Scale bond force constants by <value>
.
setreq
Set bond equilibrium lengths to <value>
. scalereq Scale bond equilibirum lengths by <value>
.
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