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Error: There are no atoms in your system. Suggestions: #95
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You did not import oplassaa force field file in E.lt file |
You defined your monomer correctly, but it is an error to use the write_once("Data Masses") {
@atom:c1 12.0100
@atom:c2 12.0100
@atom:ha 1.0080
}
E{
write("Data Atoms") {
$atom:C01 $mol @atom:c1 0.109600 5.983000 -1.155000 0.000000
$atom:C02 $mol @atom:c2 -0.058600 5.319000 0.000000 0.000000
$atom:H03 $mol @atom:ha 0.306800 6.672000 -1.155000 -0.908000
$atom:H04 $mol @atom:ha 0.315400 4.352000 -0.117000 0.593000
$atom:H05 $mol @atom:ha 0.326800 5.072000 0.297000 -1.073000
}
write("Data Bonds") {
$bond:1 @bond:B1 $atom:C01 $atom:C02
$bond:2 @bond:B2 $atom:C01 $atom:H03
$bond:3 @bond:B3 $atom:C02 $atom:H04
$bond:4 @bond:B3 $atom:C02 $atom:H05
}
write("Data Angles") {
$angle:1 @angle:A1 $atom:C02 $atom:C01 $atom:H03
$angle:2 @angle:A2 $atom:C01 $atom:C02 $atom:H04
$angle:3 @angle:A2 $atom:C01 $atom:C02 $atom:H05
$angle:4 @angle:A3 $atom:H04 $atom:C02 $atom:H05
}
write("Data Dihedrals") {
$dihedral:1 @dihedral:D1 $atom:H04 $atom:C02 $atom:C01 $atom:H03
$dihedral:2 @dihedral:D1 $atom:H05 $atom:C02 $atom:C01 $atom:H03
}
} And polymer.lt import "E.lt"
write_once("Data Boundary") {
0.0 30 xlo xhi
0.0 30 ylo yhi
0.0 30 zlo zhi
}
Polymer {
E1 = new E
E2 = new E.rot(120,-0.664,1.155,0).move(1.2,-2.21,0)
write("Data Bonds") {
$bond:5 @bond:B1 $atom:E1/C02 $atom:E2/C01
}
}
mol = new Polymer I have compiled with: |
PS the More generally, the force field for the polymer should also include at least the angle and dihedral terms involving the extra |
Hello, I followed the tutorial, but made a mistake like this
Command:moltemplate.sh polymer.lt
Please help me if you have time. Thank you!
polymer.lt
:import "E.lt"
write_once("Data Boundary") {
0.0 30 xlo xhi
0.0 30 ylo yhi
0.0 30 zlo zhi
}
Polymer inherits E{
E1= new E [1]
E2=new E [2].rot(120,-0.664,1.155,0).move(1.2,-2.21,0)
write("Data Bonds") {
$bond:5 @bond:B1 $atom:E1/C02 $atom:E2/C01
}
}
E.lt:
E{
write("Data Atoms") {
$atom:C01 $mol:E @atom:c1 0.109600 5.983000 -1.155000 0.000000
$atom:C02 $mol:E @atom:c2 -0.058600 5.319000 0.000000 0.000000
$atom:H03 $mol:E @atom:ha 0.306800 6.672000 -1.155000 -0.908000
$atom:H04 $mol:E @atom:ha 0.315400 4.352000 -0.117000 0.593000
$atom:H05 $mol:E @atom:ha 0.326800 5.072000 0.297000 -1.073000
}
write_once("Data Masses") {
@atom:c1 12.0100
@atom:c2 12.0100
@atom:ha 1.0080
}
write("Data Bonds") {
$bond:1 @bond:B1 $atom:C01 $atom:C02
$bond:2 @bond:B2 $atom:C01 $atom:H03
$bond:3 @bond:B3 $atom:C02 $atom:H04
$bond:4 @bond:B3 $atom:C02 $atom:H05
}
write("Data Angles") {
$angle:1 @Angle:A1 $atom:C02 $atom:C01 $atom:H03
$angle:2 @Angle:A2 $atom:C01 $atom:C02 $atom:H04
$angle:3 @Angle:A2 $atom:C01 $atom:C02 $atom:H05
$angle:4 @Angle:A3 $atom:H04 $atom:C02 $atom:H05
}
write("Data Dihedrals") {
$dihedral:1 @dihedral:D1 $atom:H04 $atom:C02 $atom:C01 $atom:H03
$dihedral:2 @dihedral:D1 $atom:H05 $atom:C02 $atom:C01 $atom:H03
}
... ...
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