[AMBER] Aligning of ions and DNA

From: angad sharma via AMBER <amber.ambermd.org>
Date: Sun, 8 Jan 2023 14:30:11 +0530

Dear amber users,
Is there a way by which we can do rmsfit of DNA and ions of the trajectory
at a time for the density map plot in VMD plugin.

I am doing of rmsfit of DNA of the trajectory and then calculating the
density map of ions around DNA. In this way, it works but when I increase
the isovalue in VMD, density distribution of ions around DNA takes
spherical shape upto some isovalue then it takes the form of box structure.

Is there a way to correct this?
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Received on Sun Jan 08 2023 - 01:30:03 PST
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