AMBER Archive (2006)

Subject: AMBER: trajout script

From: Fenghui Fan (
Date: Sun Nov 05 2006 - 10:23:57 CST

Dear all,

I have the following script 1:


trajin md1.mdcrd 100 100 1
trajout 100tobeused.pdb pdb
center: 1-882 mass origin
image origin center

After I run it, I got the pdb file. However I find the
protein is already out of the water box.

But If I use the following script 2:


trajin md1.mdcrd 100 100 1 trajout restart restart -------

and then I convert the restart file to the pdb file, I find the protein is still within the water box.

Will you please make some comments on what cause the protein moving out of the box by script 1?

Best regards.

Fenghui Fan

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