[AMBER] imaging issues during RMSF

From: Sangeetha B <sangeetha.bicpu.edu.in>
Date: Fri, 30 Nov 2012 19:46:52 +0530

Dear amber users,

I am simulating a trimeric protein a with flexible C-terminal region for 50
ns. Each chain is 210 aa in length. Residues 211 and 212 are two structural
Cl- ions.
I am having imaging issues while extracting the structures and performing
any analysis. I have extracted pdb structures with different image center
Without any imaging, the chains are separated in different directions and
with different options, the location of these chains vary.

I went through the amber mailing list and with the its help, I finally
found the image commands shown below gave reasonably good structures when
Whereas, when I use this for analyzing the RMS fluctuations very strange
behavior is seen.

The ptraj script that I use for generating RMS fluctuation is as follows:

trajin md1.mdcrd 1 500 1
trajin md50.mdcrd 1 500 1
strip :WAT,Cl-
center :1-210 mass
image :1-210 bymask :1-210
center :1-423 mass
image :1-423 bymask :1-423
center :1-632 mass
image :1-632 bymask :1-632
image origin center
atomicfluct out rmsf_md50ns.out .CA byatom

When I plot the output from this script (rmsf_with_imaging.jpg) there is a
sudden increase in fluctuation at the beginning of the second chain which
starts at 213.
But when I don't use any imaging commands (rmsf_no_imaging.jpg), the rms
fluctuation does not show any such sudden increase.
I have attached the images of these plots.

Why is this this strange behavior observed?
How will I make sure which set of image center commands works better for my

Any suggestions would be very helpful.

Thank you,
With regards,
B. Sangeetha
Ph.D Scholar,
Centre for Bioinformatics,
Pondicherry University,

AMBER mailing list

(image/jpeg attachment: rmsf_with_imaging.jpg)

(image/jpeg attachment: rmsf_no_imaging.jpg)

Received on Fri Nov 30 2012 - 06:30:04 PST
Custom Search