Re: amber-developers: Extra Points Calculation

From: Lachele Foley <>
Date: Mon, 10 Nov 2008 20:58:23 -0500

> Yes, it is. As far as I understand, what Lachele reported was not
> strictly a bug, but a small modification they had to do to amber7
> codes to get their lone pairs things running.

One or more alums from our lab got the code running by making modifications. I think those modifications might have been modified, too. But, it's been a long time, and I don't have an easy history to follow. The pdf was the most concrete set of instructions I had. I didn't have a file clearly marked as the modified file from which the existing EP executable was made.

I think of it as a bug... If TIP5P works, it seems to me that a molecule designed to work with TIP5P should also work. My very naive interpretation of the problem is that the original EP (LP, whatever) code was written with the assumption of small numbers of extra pairs on any one residue. But, sugars have lots of them.

> > And, why allow both EP and LP?
> Because this is how it was originally done. I think it is unneeded
> since the LP ends up being a mere alias of EP, but this does not hurt
> much.

That's the only reason I know of -- the pdf that formed the original basis for code modifications said to. I doubt we actually need it. You won't hurt my feelings a bit if you say it isn't needed and not to put it in.

> >> - max14 = 3*(nphih+nphia+ndper)
> >> + max14 = 24*(nphih+nphia+ndper)
> >
> > etc.

In one directory I found that appears to contain a number of "work in progress" versions of the extra-points code, the diffs I did show many variations on this sort of theme. I tend towards WTMI, so often hold back. Maybe I should have included all this, too...

:-) Lachele
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
Received on Fri Dec 05 2008 - 14:19:41 PST
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