On Thu, May 19, 2016 at 7:55 AM, Eiros Zamora, Juan
<j.eiros-zamora14.imperial.ac.uk> wrote:
>
> Because it’s trying to match all the backbone atoms in the trajectories (2083 atoms) to the pdb file (1729 atoms).
>
> Any idea on how to tell cpptraj to ignore the regions that are not present in the reference structure?
You will have to specify two masks, one for your target and one for
your reference so that the atoms match up. For example, if residues
1-10 and 20-30 in your target match up to residues 32-42 and 56-66 in
your reference you would specify:
rms :1-10,
20-30.CA,C,O,N,H :32-42,
56-66.CA,C,O,N,H out rms.dat mass
ref [pdb_ref]
Hope this helps,
-Dan
>
> Thanks for any suggestions,
>
> Juan
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Received on Thu May 19 2016 - 08:00:04 PDT
