AMBER Archive (2007)

Subject: Re: AMBER: PME and counter ions

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Dec 18 2007 - 12:36:38 CST

> We are simulating a protein of ~7500 residues using PME with pmemd. It
> is quite negatively charged, so we added ~250 counter ions (Na+) with
> the Leap (function addIons). The protein is really unstable, which is
> not what we expected.

Did you add water too?

Bill
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu