Table of Contents

Run 3-steps minimization

First, download the three input files needed:

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

pmemd -O -i -o min1.out -p -c rec.crd -r rec.m1.rst
pmemd -O -i -o min2.out -p -c rec.m1.rst -r rec.m2.rst
pmemd -O -i -o min3.out -p -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.h.rst > min.pdb

That's all folks!