[AMBER] atom mapping

From: Gard Nelson <Gard.Nelson.NantBio.com>
Date: Fri, 10 Jul 2015 18:38:40 +0000

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. (duhÖ) Not doing this means I canít combine the data from the two orientations since cpptraj doesnít 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 doesnít do anything. I donít suppose there is a way to input a map? I donít see anything in tleap or vmd that would do the trick eitherÖ

Thanks,
Gard
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Received on Fri Jul 10 2015 - 12:00:03 PDT
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