Hi David -
I can imagine how this might happen, as I did not have a test case and did
not build one; I might have messed up initialization somehow when you have
both ep and actually do 1-4 nb. Could you send me your test case, so I
don't have to build it? Sorry; I was worried about this but so happy to
just get the darn stuff working that I kind of forgot.
Regards - Bob
----- Original Message -----
From: "David A. Case" <case.scripps.edu>
To: <amber-developers.scripps.edu>
Sent: Monday, April 23, 2007 9:55 PM
Subject: Re: amber-developers: pmemd with extra points, early release code
ready
> 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.
>
> ...regards...dave
>
>
Received on Wed Apr 25 2007 - 06:07:26 PDT
