I should mention I create this PDB file with using this script.
parm 1WJB-OPC-FF10-folded.top
trajin 1WJB-OPC-FF10-folded.prod1.traj 1 1 1
strip :WAT
strip :Na+
strip :Cl-
trajout ref-folded.pdb
go
On Mon, Oct 17, 2016 at 2:27 PM, Parviz Seifpanahi Shabane <sparviz.vt.edu>
wrote:
> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Mon Oct 17 2016 - 12:00:02 PDT
