AMBER Archive (2009)

Subject: Re: [AMBER] ambertools for NAMD

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu May 07 2009 - 09:09:55 CDT

On Thu, May 07, 2009, Carlos Simmerling wrote:

> I worry that you get a "parm file in amber 7" message- that's pretty old.

Believe it or not, we introduced the "new" prmtop format way back in Amber 7.
So, when VMD says "parm7", it means "parm7 or later", as opposed to the "old",
Amber6-and-earlier, prmtop format.

> the HW-HW are likely water.

I agree, and these may be treated specially in NAMD. But I'm hoping there are
NAMD users on the list who will know for sure what is going on.

...dac

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