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
box.
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
(
https://www.dropbox.com/s/kmndaeeee07znk0/d.png?dl=0).
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,
Atila
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Received on Thu Jan 15 2015 - 11:00:02 PST
