AMBER Archive (2008)

Subject: AMBER: 2D-RMSD

From: Tom McGrory (tomsgotchud_at_hotmail.com)
Date: Wed Apr 23 2008 - 10:00:57 CDT

Hi,I am invertigating protein motion at high pressure. I have been using amber quite successfully. One problem I have hit in the analysis is the 2D-RMSD. I want to overlay the frames in my trajectory on a particular residue (say res A), and then calulate the 2D-RMSD of another residue (res B), so that it would give me the RMSD of res B, with respect to res A. It is my understanding that when the 2D-RMSD command is used, it overlays the frames on the residue you are calculating the 2D-RMSD of, and returns the RMSD. So in my case, it would only give the RMSD of res B, with respect to itself. Is there any way around this?Thanks,Tom McGrory
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