Hi,
Could you send me (off-list) the topology file and a few frames of the
trajectory (the ones that still seem to have imaging issues, looks
like around frame 250) so I can further debug what's going on? Also,
could you send me (also off-list) the entire output from cpptraj?
Thanks! I'll try to track down what is going on ASAP.
-Dan
On Tue, Nov 6, 2012 at 3:52 PM, Brown, Kyle <kyle.l.brown.vanderbilt.edu> wrote:
> Hi Guys,
> Thank you so much for your help. I am sorry to report that autoimage in
> ccptraj was not a panacea for my IMAGE conundrum. Attached you can view
> the rms for the entire system and for residue 165. There still seems to
> be something amiss. My input files was as follows:
>
> trajin ../100.mdcrd.gz
>
> .
> .
> [sic]
> .
> .
> trajin ../128.mdcrd.gz
> trajin ../129.mdcrd.gz
> trajin ../130.mdcrd.gz
> reference min.rst
> autoimage
> rms reference out R165rms.out :165
> rms mass out nwrms.out :1-600
> atomicfluct out back.txt .C,CA,N byres bfactor
> strip :WAT
> average ccp_avg.pdb pdb
>
> Thank you in advance for your suggestions.
> KB
>
>
> On 11/6/12 2:36 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
>
>>Hi,
>>
>>Just to add on to what Dave said, if you do use the autoimage command
>>that should be the only command you need, so your script would become:
>>
>>reference min.rst
>>autoimage
>>rms reference out R165rms.out time 0.01 :165 name R165rms
>>rms mass out nwrms.out time 0.01 :1-600 name mwrms
>>atomicfluct out back.txt .C,CA,N byres bfactor
>>strip :WAT
>>average avg.pdb pdb
>>
>>I recommend you try it on a subset of your trajectory first (ideally a
>>small range of frames where you know imaging is a problem). Let me
>>know if you run into problems.
>>
>>-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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>>
>
>
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--
-------------------------
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 Tue Nov 06 2012 - 15:30:03 PST
