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run_3-steps_minimization

Run a 3-step energy minimization

First, download the three input files needed:

  • min1.in. Energy minimization of hydrogen atoms only
  • min2.in. Energy minimization of water molecules and ions
  • min3.in. Energy 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 you need to generate a pdb file to compare/visualize the results of the E minimization:

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

That's all folks!

run_3-steps_minimization.txt · Last modified: 2018/06/19 07:05 by root