SQM calculations

Semiempirical QM calculations can now (Amber11 or newer) be performed with the AmberToos program sqm.
It is described in the AmberTools13 manual.

It is run with
sqm -O -i sqm.in -o sqm.out

This is a sample input file (note the blank before "/" on line 4):

Truncated Octa-acid after AM1 opt, 4/3-14
   qm_theory="PM6-DH+",maxcyc=0,qmcharge= 0,
    8 O    0.000    0.000    0.114
    1 H    0.000    0.754   -0.458
    1 H    0.000   -0.754   -0.458

If maxcyc is skipped, a geometry optimisation is performed.

Changepdb, command sq can generate input for it from a pdb file