topology_reorder_atoms bug

[C. Va'rnai]

Dear All,

Trying the built in topology generator for QM/MM calculation, I have found 
a bug in the topology_reorder_atoms. It reorders the atoms, but only the 
isolated atom list is updated, not the QM atoms and LINK atoms.

I've modified the topology_reorder_atoms subroutine in order to update the 
qmmm_env_mm section and the force_env section which is used to read in the 
qmmm_env_qm. Because of that new variables are needed for the 
topology_reorder_atoms (qmmm, qmmm_env_mm, force_env_section), therefore 
also the call of the subroutine in the topology.F should have been 
modified.

I've uploaded the modified latest (=downloaded last night) topology_util.F 
and topology.F files with the model input files and the test coordinate 
file, please find them in ReorderAtoms.tar. I've used the CHARMM22 force 
field file and the basis set and potential files given in the tests/ 
directory.

Best regards,

Csilla