Thank you Dan,
Yes, jumping is the problem. Should I call up cpptraj as ptraj? i.e.
cpptraj xxx.prmtop < xxx.cpptraj > xxx.log &
Many thanks,
Annie
> Date: Thu, 26 Jul 2012 20:02:50 -0600
> From: daniel.r.roe.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Error in ptraj analysis after using iwrap=1
>
> Hi,
>
> On Mon, Jul 16, 2012 at 7:25 AM, Catein Catherine
> <askamber23.hotmail.com> wrote:
> > However, when I do
> > rms first out xxx_all.rms .CA,C1
> >
> > atomicfluct out xxx.bfactor byres bfactor
> >
> > I found the profile is very strange. Please kindly refer to my attached excel files for the profiles.
>
> To show things like this it is probably better to either attach a JPG
> (or similar) format plot or the raw XY data (at least for me since I
> don't have MS office installed).
>
> Does "strange" mean the RMS makes large jumps every now and then,
> corresponding to imaging artifacts? If so you could update to the
> latest version of AT12 (bugfix.16) which introduces a new command to
> cpptraj, 'autoimage', which may do a better job imaging your
> trajectory. To use, simply specify 'autoimage', e.g.:
>
> trajin mdcrd
> autoimage
> trajout imaged.nc netcdf
>
> Hope this helps,
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> 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)
>
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Received on Fri Jul 27 2012 - 10:30:03 PDT
