AMBER Archive (2004)

Subject: AMBER: nmode with mm/pbsa

From: Nan Lin (
Date: Wed Jun 09 2004 - 20:18:15 CDT

I am trying to calculate entropy by nmode through mm/pbsa. What I want to do is to cut a 8 A sphere around the ligand ( it's a complex with protein and ligand) from the MD snapshot. I used carnal to do that. But I also need a corresponding topology file with atoms only in 8 A range. How can I do that? I checked rdparm, but don't know how to do that. I also tried recreating topology file by tleap. But it didn't work since tleap add extra hydrogens after the original bond between residues have been broken. Please let me know if you have any suggestions or solutions.
Your help is highly appreciated!

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