Re: [AMBER-Developers] Improper rules

From: David A Case <case.biomaps.rutgers.edu>
Date: Fri, 6 May 2011 10:36:53 -0400

On Mon, May 02, 2011, B. Lachele Foley wrote:

> In another email, DAC said:
> > The criterion is this: the central atom is always at position 3; positions 1,2
> > and 4 are filled in alphabetical order by atom type.
>
> I agree wholeheartedly that this sounds like a perfectly reasonable
> rule. However, I do not believe that any of the leaps are following it.

Is the problem solely with wild cards, or can you provide an example where
a non-wild-card improper is wrong? I think(?) parm99.dat has all specific
impropers in alphabetical order. I haven't checked other ff files.

>
> When was the last time this alphabetical-order rule was enforced? We
> are leaning heavily toward getting rid of wild cards altogether.

hear, hear!

...dac 

-- 
================================================================
David A. Case                     | email:                      
BioMaPS Institute and Dept. of    |     case.biomaps.rutgers.edu
    Chemistry & Chemical Biology  |    fax:      +1-732-445-5958
Rutgers University                |    phone:    +1-732-445-5885
610 Taylor Rd.                    |                             
Piscataway, NJ 08854-8087   USA   | http://casegroup.rutgers.edu
================================================================
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Fri May 06 2011 - 08:00:04 PDT
Custom Search