Well, I hope by now we all have a sense of humor about this. Foam rubber
nails; not to worry, you are not working for Microsoft. Actually, given
your excerpt below, I think I slightly misread your comments, and in
combination with following comments by Carlos, was led down a path of
worrying that you were saying the prmtop excluded list was superfluous and
should be dropped. Now not to get Carlos jumping on me for heaven's sake.
What he said was:
-- Begin quote --
Tom,
I think that's fine as long as you repack the list and don't rebuild it
from bonds, etc.
you can't assume that you know what's in the original list.
Yong suggests that you throw the list out and make a new
one.
carlos
-- End quote --
Now the "Yong suggests that you throw the list out" could be read as "Yong
suggests that the prmtop list should just be thrown out (ie., dropped from
the prmtop)", whereas, on rereading, it is now clear to me that the import
of the whole statement was that Yong was not making suggestions, but
instead
trying to figure out what the heck Darden is doing. Part of the problem
here is I figured you were introducing new ff stuff, but misread that you
were thinking about whacking the prmtop, as opposed to the reality which
was
that you were not sure what the heck the code actually does. Darden
should
answer your question.
Okay, my last mail should clarify my concerns, and that I realize there
was
a misreading in this sequence. We all sometimes fail in clarity on both
ends, reading and writing ;-)
As far as crucifying Darden, that might be a bad idea for me, as he is now
the primary source of my paycheck. Besides, in something like four years,
I
have not found a single bug that he put in shipped code, so I have to cut
him some slack on s/w engineering issues just on that account ;-)
Best to all. Let's put some freaking ff and version stamps in the prmtop
and inpcrd, add flags to the inpcrd, let everyone in the group know in
advance if we are proposing any changes to file formats, and if specific
ff
implementations require special interpretation past the interpretation
used
for amber '94, let's create some small repository of documentation,
perhaps
in the product tree unless you all don't want to tell the world, and get
the
ff dev guys or the md guys that evolved the existing parameters into
something like a ff with extra points to provide a little documentation.
If
that had been done for this extra points stuff, this whole series of 40
emails would have been unnecessary.
- Bob
----- Original Message -----
From: "Yong Duan" <duan.ucdavis.edu>
To: <amber-developers.scripps.edu>
Sent: Saturday, November 12, 2005 5:38 PM
Subject: RE: amber-developers: Excluded list ?
> ...
>> the way I originally read Yong's mail, it sounded to me like
>> he was saying,
>> and proposing, that we could drop the excluded list from the
>> prmtop.
>
> Bob, I really have to clarify this.
>
> Quite contrary, I did not propose anything. Let me quote my original
> e-mail
> here to make sure we are talking about the same e-mail.
>
> ******************
> 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 :(.
>
> ***************
>
> Did I "propose" anything? Tell me, line by line, which part made you
think
> that way.
>
> Let me re-iterate. Sander already droped the excluded list from prmtop
> since
> AMBER 7.0 when extra-points were added.
>
> Bob, I thought you were going to crucify the guy who did this. Are you
> still
> going to do this? It is now even easier since Tom is a lot closer to you
> than I am. Tom, be careful, hide somewhere. I don't think it is wise to
> let
> you see Bob any time soon. We really do not want bad things happen to
you.
>
> Now, back to my original question. Can somebody out there tell me how
can
> I
> add a pair of atoms on the excluded atom list and expect sander to use
it?
> I
> do not want to change the code for this simple thing (I am also
terrified
> that somebody may crucify me if I touch the code).
>
> By the way, does it really have to be this hard to get a little "user
> support" from our own team? This is awful!
>
>
> Yong
>
>
Received on Wed Apr 05 2006 - 23:49:48 PDT
