As I indicated before, if you want to load a reference structure you
just need to make sure you load a corresponding topology and make
'reference' use that. You can also use tags to make the typing a bit
easier. So something like:
parm 1WJB-OPC-FF10-unfolded.top
trajin 1WJB-OPC-FF10-unfolded.prod1.traj
parm 1WJB-OPC-FF10-folded.top [RefParm]
reference 1WJB-OPC-FF10-folded.prod1.traj 1 parm [RefParm]
nativecontacts reference ...
To get some more experience with how cpptraj deals with topologies etc
you may find it useful to look over some of the basic tutorials here:
http://ambermd.org/tutorials/#analysis, particularly C0 and C1.
There's also an example of parameter/reference tagging given in the
"General Concepts" part of the cpptraj chapter in the Amber 16 manual.
-Dan
On Mon, Oct 17, 2016 at 3:09 PM, Parviz Seifpanahi Shabane
<sparviz.vt.edu> wrote:
> Thank you again, Dan. problem is, I want to use the structure from folded
> (as I mentioned at first email I have to different simulation for one
> protein one start from the folded structure, another start from the
> unfolded structure) as a reference for the unfolded case. it means my
> script will be something like this.
>
> parm 1WJB-OPC-FF10-*un*folded.top
> reference 1WJB-OPC-FF10-folded.prod1.traj 1
> trajin 1WJB-OPC-FF10-*un*folded.prod1.traj
> nativecontacts ...
>
> I am getting an error from the script look like the above script not that
> one you mentioned (I run that script and get a result without problems).
> Best
> Parviz
>
>
> On Mon, Oct 17, 2016 at 2:55 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> 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
>> >>>
>> >>
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> 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
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 - 12:30:04 PDT
