Re: [AMBER] atom mapping

From: Daniel Roe <>
Date: Sun, 12 Jul 2015 09:30:33 -0600

Hi, sorry for the delay in replying.

On Fri, Jul 10, 2015 at 12:38 PM, Gard Nelson <>
> 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.

I guess I'm a bit unclear on how your two systems differ. Is it that 1
system is 'Monomer1, Monomer2, Ligand', and the other is 'Monomer2,
Monomer1, Ligand'? If so you can reorganize the system with cpptraj but it
is a bit convoluted. What I would do in this case to get the second system
in the same order as the first is split the second system into parts and
then put it back together using COORDS data sets:

parm myparm.parm7
loadcrd M1 # Name this COORDS set 'M1'
crdaction M1 strip <mask that selects everything but M1>
loadcrd M2 # Name this Coords set 'M2'
crdaction M2 strip <mask that selects everything but M2>
loadcrd Ligand # Name this Coords set 'Ligand'
crdaction Ligand strip <mask that selects everything but Ligand>
# Combine parts in the order you want.
combinecrd M1 M2 Ligand crdname NewSystem2
crdout NewSystem2

Hopefully I've understood your issue correctly. If not let me know, and
feel free to send me off-list files that illustrate your problem. Good luck,


> 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
> 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

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Sun Jul 12 2015 - 09:00:02 PDT
Custom Search