Another thought is you could fake a pdb that matches what you want to
fit, making sure that the atoms that you want to fit to have real
coordinates, while the rest could be 0's.
Bill
On 5/19/16 7:37 AM, Daniel Roe wrote:
> 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 - 12:30:04 PDT
