A few comments.
On Mon, Oct 17, 2016 at 2:37 PM, Parviz Seifpanahi Shabane
<sparviz.vt.edu> wrote:
> "Error: PDB ref-folded.pdb: No frames read. atom=844 expected 46766."
This is because there are fewer atoms in ref-folded.pdb than in the
topology you are trying to load with, 1WJB-OPC-FF10-folded.top (all
coordinates in cpptraj get associated with a loaded topology). If you
really wanted to use that PDB as a reference you would do something
like:
parm ref-folded.pdb
reference ref-folded.pdb parm ref-folded.pdb
However, since it seems you created the reference from
1WJB-OPC-FF10-folded.prod1.traj anyway, why not just use that as the
reference?
parm 1WJB-OPC-FF10-folded.top
reference 1WJB-OPC-FF10-folded.prod1.traj 1
trajin 1WJB-OPC-FF10-folded.prod1.traj
nativecontacts ...
or better yet just use the 'first' keyword in the 'nativecontacts'
command to specify you want to use the first frame as a reference?
-Dan
> 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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--
-------------------------
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 - 12:00:02 PDT
