[AMBER] unusual structure after heating. why?

From: Atila Petrosian <atila.petrosian.gmail.com>
Date: Thu, 15 Jan 2015 22:01:04 +0330

Dear Jason

Thanks for your quick answer.

After using Amber Coordinates with box for mdcrd file, the privious problem
was solved. But there are 2 new points. please note the figure in the
following link (https://www.dropbox.com/s/e8a76gzzmv16r3n/c.png?dl=0):

1) Water molecules are shown as a triangle (there is a bond between
Hydrogen atoms). I don't know the reason of this issue.

2) Most of water molecules have went out of box. To solve this issue,
I re-imaged molecules back into the box as follows:

trajin prod.mdcrd
trajout prod-reimage.mdcrd
center :1-98
image familiar

When I see prod-reimage.mdcrd file using vmd, water molecules back into the
There are 2000 frames in mdcrd file. In more precise view, I found that in
two frames (1084 and 1085), protein molecule have went out of box. please
note the figure in the following link

I re-imaged molecules, so what is the reason of that protein molecule goes
out of box in two frames during the trajectory?

I calculated rmsd. rmsd values are very high in these two frames.

How to resolve this problem?

Best wishes,
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Received on Thu Jan 15 2015 - 11:00:02 PST
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