Dear Amber Users:
We have problems with ptraj image.
The protein moved out of the box after the actions of "center" and "image". This is the script I used:
trajin prod.mdcrd
center :1-462
image origin center familiar
trajout prod_imaged.mdcrd
If I use the following script in which I deleted the command line "center :1-462", the imaged protein remains within the box.
trajin prod.mdcrd
image origin center familiar
trajout prod_imaged.mdcrd
However, when I search online or read AMBER manual or tutorial, they all suggested I need to center my solute first and then image. Could anybody please tell me whether we should center solute first or not. And if we do not center the solute first, is the imaged file reliable as we want to calculate some water molecules around certain residues.
Thank you so much.
Yufang
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Received on Tue May 11 2010 - 17:00:03 PDT
