[AMBER] big cavity in the trajectory

From: Tong Zhu <tongzhu9110.gmail.com>
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?


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(image/png attachment: ______.PNG)

Received on Fri Jan 30 2015 - 00:30:02 PST
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