AMBER Archive (2008)

Subject: Re: AMBER: Help in radii

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Jan 16 2008 - 14:31:07 CST

Quoting snoze pa <snoze.pa_at_gmail.com>:

> I am getting following error message after running a small Gaussian
> calculation.
> *
> No NMR shielding tensors so no spin-rotation constants.
> Leave Link 601
> (Enter g03/l602.exe)
> Merz-Kollman atomic radii used.
> Atom Element Radius
>
> [...]
> 14 26 0.00
> GetVDW: no radius for atom 14 atomic number 26.
> Error termination via Lnk1e in g03/l602.exe
> *
> How can I get the GetVDW for atomic no 14 in Gaussian. Do I need to
> mention it in the beginning of the input Gaussian file
> like Pop=(ReadRadii)! Any help. Thanks in advance

In R.E.D., this problem is automatically handled & the input is
automatically generated... You can also modify the source code, and
change the Fe radii if you do not like the "1.8" value set by default.

> What is the actual radii of Fe shall i use? in amber archive i saw somebody
> was suggesting 0.49
> http://structbio.vanderbilt.edu/archives/amber-archive/2004/2749.php
> while FyD notebook it is recommended to use larger one like 2.0 etc. The
> program like vmd suggest 2.01 while in gammes it is 1.8 Which one is the
> right one. thanks in advance

Why not doing some testing: Are you sure this radii strongly affects
the Fe charge value ? Did you test that ?

regards, Francois

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