[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

This e-mail message and any attachments are only for the use of the intended recipient and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If you are not the intended recipient, any disclosure, distribution or other use of this e-mail message or attachments is prohibited. If you have received this e-mail message in error, please delete and notify the sender immediately. Thank you.
AMBER mailing list
Received on Fri Jul 10 2015 - 12:00:03 PDT
Custom Search