[gmx-users] atom numbers in top file

[Shima Arasteh]

Dear gmx users,

I have modified the top file of my input.pdb. In this modification I have deleted 2 atoms, bonds, and diedrals which these deldeted atoms are involved. The atom numbers of deleted atoms are 2 and 3.
IN grompp I get a fatal error that the top file has not a consecutive numbers and doesn't start from 1.
Would it be possible to solve this problem? Am I supposed to renumber the atoms and other things manually? Is there any command to renumber the top file? Or is there any other solutions?

your suggestions would be appreciated.

 
Sincerely,
Shima