Error: There are no atoms in your system. Suggestions:

[Yong-Q]

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 } ... ...

[hu-fu1]

You did not import oplassaa force field file in E.lt file

[hothello]

You defined your monomer correctly, but it is an error to use the import E statement, as this is only used for LT files containing force field parameters. The error you reported appears because you defined a polymer, but actually never create any instance of it. The revised files are: E.lt

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: moltemplate.sh -nocheck polymer.lt as the terms coefficients are not defined. I hope this helps.

[hothello]

PS the -nocheck option is necessary because a bond is defined, but the bond_coeff @bond:B1 is not.

More generally, the force field for the polymer should also include at least the angle and dihedral terms involving the extra $bond:5 term. I assume that yours is a toy model to learn the syntax.