delete_atoms command

Use delete bonds to delete the interactions involved with the atoms that you want to delete. The use delete atoms.


Assuming you get the error about missing dihedral


after using delete_atoms, then my assumpution

would be you deleted atoms that are part of a dihedral,

or the ensuing dynamics is bad enough that one or more

dihedrals blew apart.


Thank you. I used “mol yes” keyword to delete all other atoms in the same molecule ID. Therefore, there should not be any dihedral in deleted molecules. please help me to solve this problem.

Did you try “delete_bonds” and then delete those atoms, as Arun mentioned in the earlier post?


Dear Arun, Steve and Kasra

Thanks a lot for your attentions. I used delete_bonds then delete_atoms
command for the specified group of atoms. but the error is still there.
Apparently all of dihedrals between deleted atoms in the group and other
atoms is not removed. Any suggestion will be appreciated.

delete_bonds cy multi
delete_atoms group cy mol yes