AMBER Archive (2009)

Subject: [AMBER] DNA as well as protein distorted during MD run in sander

From: Jayalakshmi Sridhar (
Date: Tue Jun 09 2009 - 09:30:39 CDT

I am new to Amber. I have installed amber10 on a redhat linux machine. I am having problems with MD with sander. I am running the first tutorial of the DNA in MD as per the instructions. Minimization runs well. But when I try the MD, the DNA gets completely distorted. All the bonds in the DNA are stretched out. I am using the *.in files given in the tutorial. I am having the same trouble with my proteins too. Could there be nay problem with sander installation? Where do I look for trouble shooting. Help is greatly appreciated.

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