You can specify reference mask
Check this link for example
https://github.com/Amber-MD/cpptraj/blob/1a6ceaa7703c9d694c6b0717cf2c2c8f05353469/test/Test_General/RunTest.sh#L38-L39
Hai
> On Nov 16, 2016, at 6:02 PM, anu chandra <anu80125.gmail.com> 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 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
> Anu
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Received on Wed Nov 16 2016 - 15:30:03 PST
