Date: Fri, 30 Jan 2015 16:29:01 +0800
Dear amber users,
I want to image my trajectory to the original box using cpptraj. The input
file is :
trajin ch2o_prod_v0_l0.crd 1 30000 30
center :1 origin
reference ch2o.rst
center :1
image center familiar
rms reference :1 out backbone_rmsd_ppc.dat
trajout image.crd
However, I found a great cavity (without any water molecules) in the imaged
trajectory (please see the attached picture). Could you please tell me how
can I fix this problem?
Tong,
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(image/png attachment: ______.PNG)
