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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 18 2012 - 08:30:02 PDT
