AMBER Archive (2004)

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

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Apr 20 2004 - 15:28:13 CDT

Dear Mr. Case,

The file I am using is, as I said before, from CCD Database. The name of
the molecule is CYTIDI10. I used the following command to convert to mol2
file to see whether there is a problem in antechamber conversion or not:

    $ antechamber -i CYTIDI10.pdb -fi pdb -o CYTIDI10.mol2 -fo mol2

and the error was

     Warning, 22 bond types may not be correctly assigned.

It gave a .mol2 file but totally wrong structure, projected on a 2D
surface. Is there any way to solve this problem? Or do I have to create
the gaussian input file using a different procedure?

Best, 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       - Home Address:                -
  - University of Rochester      -                              -
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On Mon, 19 Apr 2004, David A. Case wrote:

> 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
>
>

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