Run 3-steps minimization

First, download the three input files needed:

• min1.in. Minimization of hydrogen atoms only
• min2.in. Minimization of water molecules and ions
• min3.in. Free minimization of the whole system

Now, let your already prepared files be rec.top and rec.crd. Execute the following sequence of commands:

pmemd -O -i min1.in -o min1.out -p rec.top -c rec.crd -r rec.m1.rst
pmemd -O -i min2.in -o min2.out -p rec.top -c rec.m1.rst -r rec.m2.rst
pmemd -O -i min3.in -o min3.out -p rec.top -c rec.m2.rst -r rec.h.rst

Now if you need a pdb to compare visualize the results of the minimization:

ambpdb -p rec.top < rec.h.rst > min.pdb

That's all folks!