AMBER Archive (2009)

Subject: RE: [AMBER] ambertools for NAMD

From: Wei Huang (
Date: Thu May 07 2009 - 09:51:06 CDT

For NAMD, I don't think so. It depends on how you prepare the input files.

In the topology file for TIP3 water, there is a line said you need to have
H1-H2 bond if SHAKE is used.
"!BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake"

Jorgen, could you tell us details about how you prepare the input files?


-----Original Message-----
From: [] On Behalf
Of Andrew Purkiss-Trew
Sent: Thursday, May 07, 2009 9:30 AM
To: AMBER Mailing List
Subject: Re: [AMBER] ambertools for NAMD

On Thu, 2009-05-07 at 10:09 -0400, David A. Case wrote:
> On Thu, May 07, 2009, Carlos Simmerling wrote:
> > I worry that you get a "parm file in amber 7" message- that's pretty
> Believe it or not, we introduced the "new" prmtop format way back in Amber
> So, when VMD says "parm7", it means "parm7 or later", as opposed to the
> 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
> NAMD users on the list who will know for sure what is going on.

>From memory, NAMD treats TIP3P-like water differently to Amber.

Amber uses three bonds (with Shake to constraint all the distances, 2 x
OW-HW and one HW-HW)

NAMD, by default, uses the HW-OW-HW bond angle and the 2 OW-HW distances
to do the same thing.

There was a way to force Amber-like behavior, but I can't remember what
it was off the top of my head. There should be instructions in the NAMD
documentation, try looking for 'use of Amber force field'

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