Dr. Case,
Thanks for your reply. So you are saying atoms pairs such as nc/nd and
cc/cd are of the same type, but in the context of bond angles and
torsions, they are different due to conjugation (conjugated single or
conjugated double bond)?
Lihua
On Thu, 14 Apr 2005, David A. Case wrote:
> Date: Thu, 14 Apr 2005 23:02:48 -0700
> From: David A. Case <case.scripps.edu>
> Reply-To: amber.scripps.edu
> To: amber.scripps.edu
> Subject: Re: AMBER: parameters in gaff.dat
>
> On Fri, Apr 15, 2005, Lihua Wang wrote:
>>
>>
>> 2. If two atom types are 'identical' as indicated in gaff.dat, can i
>> suppose that they are interchangeable? if they are truly identical, why
>> are some parameters that are supposed to be 'identical' vastly different?
>> For example:
>>
>> nd-cc-nh are nc-cd-nh are 72.4 120.11 while
>> nc-cc-hn and nd-cd-nh are 73.9 111.94
>
> Since, as you point out, the parameters are quite different, I don't
> understand why you are convinced that the atom types themselves are
> "identical".
>
> In any event, the rationale and use of cc/cd pairs (and others like that)
> is explained in detail here:
>
> %A J. Wang
> %A R.M. Wolf
> %A J.W. Caldwell
> %A P.A. Kollman
> %A D.A. Case
> %T Development and testing of a general Amber force field
> %J J. Comput. Chem.
> %V 25
> %P 1157-1174
> %D 2004
>
>
> ....dac
>
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Received on Fri Apr 15 2005 - 19:53:00 PDT
