[AMBER] cpptraj RMSD calculation with mismatch residue numbers

From: anu chandra <anu80125.gmail.com>
Date: Thu, 17 Nov 2016 04:32:04 +0530

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 ABdomain.top [AB]
parm Bdomain.top [B]

trajin 1md.nc parm [AB]
trajin 2md.nc parm [AB]
trajin 1md.nc parm [B]
trajin 2md.nc 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
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Received on Wed Nov 16 2016 - 15:30:02 PST
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