AMBER Archive (2003)

Subject: Re: AMBER: missing of VdW Parameters for N3

From: wendy.cornell_at_pharma.novartis.com
Date: Wed Dec 03 2003 - 09:18:23 CST

I was previously not aware of this mismatch with the N3 VDW parameter. It
appears to be an oversight.

Regards,
-Wendy

                                                                                                                                     
                      "David A. Case"
                      <case_at_scripps.edu To: amber_at_scripps.edu
> cc: Wendy Cornell/PH/Novartis_at_PH
                                               Subject: Re: AMBER: missing of VdW Parameters for N3
                      11/21/2003 11:08
                      AM
                                                                                                                                     
                                                                                                                                     

On Fri, Nov 21, 2003, Nikolai Smolin wrote:

> I just found that in parm94.dat missed Van der Waals Parameters for
> atom type N3.
> And for this type Leap used parameters from N type
> just 1.824 for radius, but not 1.875 which value described
> in paper Cornell and all. J. Am. Chem. Soc. 117 5179 1995.
>

In all versions of parm94.dat since amber4.1, atom type "N3" has been
equivalenced to atom type "N", so that they share the same van der Waals
parameters. Apparently the changes discussed in footnote "n" of Table 14
of the above paper were never incorporated into any distributed parameter
files, at least as far as I can tell.

So, a decade of de facto usage means that the van der Waals radius of N3
in Cornell et al. is really 1.824, in spite of what it says in the paper.

I'm cc-ing this to Wendy Cornell, in case she has knowledge of this, or I
am missing something.

..regards...dac 

--

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David A. Case                     |  e-mail:      case_at_scripps.edu
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