Re: [AMBER] cpptraj RMSD calculation with mismatch residue numbers

From: Daniel Roe <>
Date: Wed, 30 Nov 2016 16:07:00 -0500


Sorry for the long delay on this.

Since you essentially have two different systems here your best bet is
probably to calculate the rmsd in two separate runs, then concatenate
the data like so:

parm [AB]
parm [B]
# Get first frame of AB as reference
reference parm [AB] 1
# Load AB trajectories
trajin parm [AB]
trajin parm [AB]
# RMSD of B in AB
rms AB reference :101-200
# Clear the AB trajectories
clear trajin
# Load B trajectories
trajin parm [B]
trajin parm [B]
# RMSD of B; first mask is target, second is reference
rms B reference :1-100 :101-200
# Concatenate and write out
dataset cat AB B name AB-B
writedata AB-B.agr AB-B

Hope this helps,


On Wed, Nov 16, 2016 at 6:02 PM, anu chandra <> wrote:
> Dear Amber users,
> I am working with a two domain protein, A domain (residue 1 -100) and B
> domain (101-200). After 100 ns simulation of two domains together, I
> removed the A domain and continued the simulation for another 100 ns ( For
> this purpose, I basically generated a new system with conformation of B
> domain obtained after 100 ns simulation of AB domain together). In the
> second set of simulation, since the A domain was removed the residue
> numbering for B domain has changed to 1 - 100.
> Now, I am trying to calculate the RMSD of B domain over whole 200 ns
> simulation time (100 + 100) with reference to the starting conformation of
> B domain (ie. at t = 0). Since there is mismatch of residue numbering in B
> domain, I just looking for a way to calculate RMSD with cpptraj. A possible
> input file should have following workflow,
> parm [AB]
> parm [B]
> trajin parm [AB]
> trajin parm [AB]
> trajin parm [B]
> trajin parm [B]
> reference ABdomain.crd parm [AB]
> #command to calculate the RMSD of B domain ( ie. residue 101-200 from first
> two set of trajectories and 1-100 from second two set of trajectories)
> Any help would be highly appreciated
> Thanks in advance
> Anu
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Wed Nov 30 2016 - 13:30:03 PST
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