Dear Catherine,
The reason Dan mentioned that is that you should probably use only one
protein in your "center" command before imaging, so change:
center :1-677 origin
to use a smaller selection (could also be just part of a protein, or a
single residue).
This should cause the imaging to put all the proteins in the same box.
--Marc
On 18 July 2012 16:14, Catein Catherine <askamber23.hotmail.com> wrote:
>
> Dear Dan,
> No, the protein I am studying is not a monomer, it compose of 2 large and
> 2 small proteins.
> Is it going to be a problem? Many thanks.
> Best regards,
> Catherine
>
> > Date: Wed, 18 Jul 2012 08:02:33 -0600
> > From: daniel.r.roe.gmail.com
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] Error in ptraj after using iwrap=1, even using
> center and image origin
> >
> > Hi,
> >
> > First, have you visualized the imaged trajectory to see if your issue
> > is actually due to imaging artifacts? In order to do this you will
> > need a much simpler script. Also, it's tough to tell because your
> > ptraj script as you posted it is jumbled (no newlines) but the
> > 'trajout' command does not accept a mask (i.e. the '.N1,C' does
> > nothing). To make things simpler just 'trajin' a small portion of
> > xxx.mdcrd where the RMSD jumps occur so you can see what is going on.
> > For example, if one of the jumps occurs within the first 50 frames:
> >
> > trajin ./xxx.mdcrd 1 50 1
> > center :1-677 origin
> > image origin center familiar
> > trajout imaged.netcdf netcdf
> >
> > Also, is your protein (residues 1-677) a monomer?
> >
> > -Dan
> >
> > On Tue, Jul 17, 2012 at 9:18 PM, Catein Catherine
> > <askamber23.hotmail.com> wrote:
> > >
> > > Dear Sir/Madam,
> > > I have done a long simulation. In order not to avoid the problem of
> outside box, I have used iwrap=1, in all my calculations.
> > > According to the previous comments I added the "center and image
> origin" to the ptraj run (1-677 represent all the protein 677 protein
> residues)
> > > trajin ./xxx.mdcrdcenter :1-677 originimage origin center
> familiartrajout yyy.netcdf netcdf .N1,CAradgyr out yyy_all.radgyr.datrms
> first out xxx_all.rms .CA,C1
> > > atomicfluct out xxx.bfactor byres bfactoratomicfluct out xxx.nobfactor
> .CA,C1 byresaverage xxx_average_nobox.pdb pdb noboxmatrix correl .CA,C1 out
> xxx.corr byreshbond distance 3.5 angle 120.0 solventdonor WAT O
> solventacceptor WAT O H1 solventacceptor WAT O H2 out xxx.WAT.hbond2
> > > I found the profile is still strange. e.g the rmsd jump up and down
> to a very large values. It seems that when the molecule is moved to fit
> the box size, it affect all the analyzing parameters.
> > > Please kindly instruct if I have using the ptraj commands wrongly.
> Many thanks.
> > > Many thanks.
> > > Cat
> > >
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Lab Specialist
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 201
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-9119 (Fax)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jul 18 2012 - 09:00:03 PDT
