Hi Daniel,
Thank you for answering, I am using amber 2015, and this the error which I
got (with or without using the strip command)
"Error: PDB ref-folded.pdb: No frames read. atom=844 expected 46766."
Best
Parviz
On Mon, Oct 17, 2016 at 1:02 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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 - 11:30:03 PDT
