Re: amber-developers: pmemd with extra points, early release code ready

From: David A. Case <>
Date: Mon, 23 Apr 2007 18:55:36 -0700

On Fri, Apr 20, 2007, Robert Duke wrote:

> Okay, I am finally done adding extra points support into pmemd. This has
> only been tested for the tip4p and tip5p water models so far.

Bob: have you done a protein + water? (or any solute?) I'm getting zero
14-NB and 14-EEL at step one of my first test case. I can send you
everything, but I thought maybe something would ring a bell (I have to go
home now....)

This is ff99SB protein (so, no extra points on the protein) + tip4p water.
The electrostatic interaction is identical between sander and pmemd, so it
looks like the extra points on the water are being handled correctly. But
the 1-4 interactions (which are in the solute) are getting zeroes out somehow.
Of course, the dynamics is then completely haywire.

I'll send more info if this is not enough.

Received on Wed Apr 25 2007 - 06:07:26 PDT
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