Hi,
On Mon, Oct 17, 2016 at 12:25 PM, Parviz Seifpanahi Shabane
<sparviz.vt.edu> wrote:
> this my input file ( I tried to strip water and ions from my trajectory and
> use the PDB file(which I strip water and ions from it too) as the reference
> but it did not work).
Could you be more specific as to how it did not work? Did you receive
an error message, etc? It would also be helpful to know the version of
cpptraj you are running.
>
> nativecontacts :1-55&!.H= writecontacts contacts.dat out numcontacts.dat reference ref-folded.pdb
You should use either 'reference' to use the first loaded reference or
'ref <name>' to use a specific reference structure by name. See the
manual entry for 'nativecontacts' for full details on all keywords.
-Dan
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Oct 17 2016 - 10:30:02 PDT
