[gmx-users] Preparing dual topology for free energy calculation

[Tushar Ranjan Moharana]

Hi Rompaey,
Thanks for your valuable advice. As per your advice I went through the
paper (
https://www.google.be/url?sa=t&source=web&rct=j&url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872215/&ved=0ahUKEwjq3I7M-YbMAhXI_w4KHQeeCX8QFggoMAU&usg=AFQjCNHnkqQys4V7UYCURTPZyKQEYrGdWQ&sig2=rpmfKD8E07TCQ_XfeUyE3Q).


They also used dual topology approach. They use pmx to generate those
topology. Unfortunately the same program didn't work for me. It gives the
following error (mentioned at the bottom) which I couldn't solve. I went
through many tutorial and on line material but everywhere people talk about
binding energy with ligand. Also they provide topology file and don't
describe how to generate one. I will be grateful if I can get some other
option to prepare dual topology or calculate free energy without dual
topology.

Error message from pmx:

Traceback (most recent call last):
  File "/home/madhu/pmx/scripts/mutate.py", line 504, in <module>
    main(sys.argv)
  File "/home/madhu/pmx/scripts/mutate.py", line 495, in main
    apply_mutation( m, mutation, mtp_file )
  File "/home/madhu/pmx/scripts/mutate.py", line 354, in apply_mutation
    apply_aa_mutation(m, residue, new_aa_name, mtp_file)
  File "/home/madhu/pmx/scripts/mutate.py", line 332, in apply_aa_mutation
    bb_super(residue, hybrid_res )
  File "/usr/local/lib/python2.7/dist-packages/pmx/geometry.py", line 168,
in bb_super
    assert len(atoms1) == len(atoms2), "%s -> %s" % ( '-'.join( map(lambda
a: a.name, atoms1)),'-'.join( map(lambda a: a.name, atoms2)) )

Thanks a lot.

"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB