AMBER Archive (2007)

Subject: Re: AMBER: Antechamber esp calculation

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Jan 23 2007 - 00:07:31 CST

Dear Mathew,

Do you have the checkpoint file of this gaussian optimization? If yes, you
can run a gaussian job to get the ESP Data points manually.

Is this .pdb file after the optimization? If yes, what is the rmsd value
compared to the original structure? (I would have expected the amino
protons to be out of plane, though)

You need to optimize the structure prior to the ESP data point
calculation. Gaussian should not change the structure too much; it will
just optimize it.

On Tue, 23 Jan 2007, mathew k varghese wrote:

> Dear amber community,
>
> I have a doubt about the parametrization of some modified nucleic acid residues.
> We are trying to generate the parameters by doing Gaussian calculation. The residues have a charge of -1. The molecule after optimzation at HF-6G* is distorted about the phosphate group. The espgen is not producing any output files from the gaussian output files. There are not any error messages also. The pdb file of the residue amd the gaussian output files are attached. Please advice me what to do.
>
> I have one more question. Is it raesonable to do a singlepoint calculation to get the esp, if it is an experimental structure?
>
> Thanking you
>
> Mathew
>
>
>
> ---------------------------------
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
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