Dear Amber users,
I'm simulating an ion channel for which I want to check if it's allowing
the ions to pass or not. Therefore, I would like to plot the Z component of
the trajectory vector for those ions.
I tried to do this in cpptraj, but I'm afraid I'm missing something.
Can someone please suggest how I can get such data?
I tried the following to create a dataset and then access the vectors and
collect the Z-axis compound, but it is not working:
vector ionsCl center :Cl- out ionsCl_axisZ.txt
dataset vectorcoord Z ionsCl name ionsCl_axisZ
run
writedata ionsCl_axisZ.dat ionsCl_axisZ
and I'm getting this kind of error message:
[vector ionsCl center :Cl- out ionsCl_axisZ.txt]
VECTOR: Type Center, mask [:Cl-], output to ionsCl_axisZ.txt
[dataset vectorcoord Z ionsCl name ionsCl_axisZ]
Warning: 'ionsCl' is empty.
Error: 'vectorcoord': No data sets selected.
1 errors encountered reading input.
Looking forward to some help!
Best regards,
Karolina Mitusińska
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Received on Mon Sep 18 2023 - 03:30:02 PDT
