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
Received on Mon Oct 17 2016 - 12:30:03 PDT
