Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations?

From: David A. Case <>
Date: Mon, 19 Apr 2004 14:45:34 -0700

On Mon, Apr 19, 2004, Ilyas Yildirim wrote:
> #HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt
> but it gave the following error in the output
> ---------------------------
> ...
> 30 O nan nan nan nan nan
> 26 27 28 29 30
> 26 O nan
> 27 O nan nan
> 28 O nan nan nan
> 29 O nan nan nan nan
> 30 O nan nan nan nan nan
> Error termination via Lnk1e in /opt/gaussian/g98/l202.exe.

> I used molden to see how the structure looks like, but it does not look
> like a normal structure.The atoms lay down on a plane which is wrong.

If you have a bad initial structure, there is not much that either Gaussian
or antechamber can do. The "nan" above in the Gaussian output means "not a
number", meaning that Gaussian totally failed to interpret your input data.

Without seeing the input file, one cannot say why this is. If you are using
antechamber to create the input file, you still need to make sure that the
Gaussian input makes sense. Antechamber is sometimes bad at recognizing bad
input data, and may go ahead and write a Gaussian input file even when it
failed to correctly parse the input pdb file. Again, it is hard to say when
so little information is provided.

> 2. How can I modify the input command line so that I do not OPTIMIZE the
> structure, but just get the ESP Data points?

Remove the "opt" keyword from the Gaussian file.

....good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Mon Apr 19 2004 - 22:53:00 PDT
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