Re: [AMBER] Image problems with IWRAP=1

From: Brown, Kyle <kyle.l.brown.Vanderbilt.Edu>
Date: Tue, 6 Nov 2012 22:52:03 +0000

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

trajin ../128.mdcrd.gz
trajin ../129.mdcrd.gz
trajin ../130.mdcrd.gz
reference min.rst
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.

On 11/6/12 2:36 PM, "Daniel Roe" <> wrote:

>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
>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.
>Daniel R. Roe, PhD
>Department of Medicinal Chemistry
>University of Utah
>30 South 2000 East, Room 201
>Salt Lake City, UT 84112-5820
>(801) 587-9652
>(801) 585-9119 (Fax)
>AMBER mailing list

AMBER mailing list

(image/png attachment: ccptraj_nwrms.png)

(image/png attachment: ccptraj_R165.png)

Received on Tue Nov 06 2012 - 15:00:03 PST
Custom Search