Thank you, David, for your response. I have used the following commands:
trajin zkm.mdcrd
autoimage
strip :WAT
strip :Cl-
trajout zkm-dry.mdcrd nobox
I have also used iwrap=1 during the simulation run. When auto-image did not work worked, I used
following
too:
1. center :1-100 mass origin (including ligand)
image origin center familiar
2. center :100 (ligand only)
image center familiar
Please let me know if I have done it correctly or not.
Thanks,
Zaid
>On Fri, Mar 01, 2019, zaid kamal wrote:
>
>I have used Amber18 and being a beginner, I am facing a problem in
>autoimaging the ligand along with the protein. In autoimage command
>only the protein is imaged and ligand dissociates far away at different
>directions. When i tried to center my ligand, then the protein
>fluctuates.
It's pretty unusual, but far from impossible, for autoimage to fail.
Can you say exactly what commands you used? If you haven't done so yet,
be sure to try "autoimage" with no arguments and no other centering
commands.
....dac
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Received on Mon Mar 04 2019 - 01:00:02 PST
