Dear Sirs,
Thank you for your all advise.
I'm sorry to have passed for a long time
I have checked all of files again, as following all your suggestions.
I summarized the result for troubles of the others.
I wrote:
> I check the resulted trajectory files by using VMD. Some very long bonds
> assigned to protein (the color is gray and blue) could be seen between the
> outside and the inside of the protein.
Carlos wrote:
>it also may be that you are not using the right format for
>the trajectory (make sure to pick Amber coordinates and
>you need to know if you have periodic box info in the file).
As the result, Carlos's opinion is correct.
The reason of display error is selection of the VMD option.
Our VMD version is 1.8.6 and the main windows are just different
from the manual B1. There are two choice to read .mdcrd file,
"AMBER coordinates" and "AMBER coordinates with periodic box".
It is not applicable to select "automatically".
I initially chose "AMBER coordinates". I don't know what is different
between two options but choosing "AMBER coordinates with periodic box"
caused right view of the molecule.
Thank you for your kind suggestion.
Miki
_/_/_/ $B<.ITI,.8!!=yITI,;`(B _/_/_/
_/_/_/ M. MAEDA _/_/_/
_/_/_/ mmaeda.nias.affrc.go.jp _/_/_/
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Received on Sun Aug 12 2007 - 06:07:23 PDT
