Date: Thu, 30 Aug 2018 00:12:19 +0000
Hello:
I am learning how to use cpptraj of Amber 16 to wrap the protein and water into the box. I am using the cellulose system from the Amber benchmark. The topology, restart and input files were downloaded from the Amber benchmark website. After cpptraj, water molecules were wrapped back into the box but the protein was not in the center. And it seems that the bottom of the box was moved to the top.
My cpptraj input(rst.cpptraj file):
trajin inpcrd
autoimage
cpptraj command:
$AMBERHOME/bin/cpptraj -p prmtop -i rst.cpptraj &>rstcpp.log -x out.crd
Is there anything wrong with my cpptraj command or input file? The picture shows the system after the cpptraj.
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(image/png attachment: after.png)
