Hi all,
I working with a homodimeric protein bound to a chiral ligand. I have simulated the ligand in two crystallographic orientations. After running the simulations, I realized that I should have swapped the numbering of the monomers in the parameter file since the chiral ligand causes each monomer to adopt a slightly different conformation. (duh…) Not doing this means I can’t combine the data from the two orientations since cpptraj doesn’t know the difference between the conformationally different monomers.
Does anyone know of a way to swap the coordinates (or alternately the atom and residue Ids) of monomer one for those of monomer two in post-processing? cpptraj's atommap command does almost what I want, except that since the two monomers are topologically identical, it doesn’t do anything. I don’t suppose there is a way to input a map? I don’t see anything in tleap or vmd that would do the trick either…
Thanks,
Gard
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Received on Fri Jul 10 2015 - 12:00:03 PDT
