Sorry, my message was not clear. I was rather surprised myself. Yes, I
meant
sander actually ignores the excluded atom list and re-builds it,
apparently
from bond, angle and dihedral lists. I think this is done when extra
points
are turned on. Looks like the LES code is gone when you turn on extra
points
(hopefully, nobody has tried this combination yet). I think the code was
changed since amber 7. I am pretty sure the exluded list was used in
amber5/6. Yes, GB code deals with this "correctly".
I can understand the need to change the excluded atom list with extra
points. But I thought it should be done in things like Leap, perhaps add
an
extra line in prep file to indicate which part is special and needs to be
dealt with in Leap. Minor modification within sander targeted exclusively
to
extra points is understandable (and perhaps acceptable). Now, it actually
affects the whole excluded list logic. This seems a bit unusual.
yong
-----Original Message-----
From: owner-amber-developers.scripps.edu
[mailto:owner-amber-developers.scripps.edu] On Behalf Of Carlos Simmerling
Sent: Thursday, November 10, 2005 5:43 PM
To: amber-developers.scripps.edu
Subject: Re: amber-developers: Excluded list ?
are you saying that sander ignores the exlusion list in the prmtop?
if so, I think that is not a good idea and should have been widely
discussed before being done. It would break a few things that
I have done. Where is that code?
carlos
Yong Duan wrote:
>Just realized that sander actually re-constitutes the excluded list from
>bond, angle, dihedral lists. Any insightful comments why it has to be
done
>this way? What will happen if I disable this (i.e., remove the code)? I
need
>some flexibility in the excluded list but don't like to break too many
>things :(.
>
>
>yong
>
>
>
Received on Wed Apr 05 2006 - 23:49:50 PDT
