AMBER Archive (2008)

Subject: RE: AMBER: resp and 99999

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Sep 05 2008 - 09:31:51 CDT

Hi Terveisin,

> I was playing around with the excellent tutorial
> http://amber.scripps.edu/tutorials/advanced/tutorial1/section1.htm
> (Tutorial A1: Setting up an Advanced System (Including Charge Derivation)
> )
>
> In the tutorial resp fitting is done with respect of a grid of
> electrostatic potential of ~94000 points.
> (the file "floBF_esp.dat", first line is 4294681, ==42 atoms, 94681
> gridpoints)
> Is there any way one can run 'resp' (of the Amber10 package) using
> more than 99999 gridpoints in the potential file?

I'm not sure I understand your question. I believe this is exactly what we
do in the tutorial already.

"The ESP Fit center is a little more complicated since there are more than
9999 and Gaussian just prints *'s here. So you can just take the difference
between the line numbers (e.g. using a utility such as nl 'nl floB_hf.gout >
floB_hf.gout_line_numbers'). In this case for floB we have 94,681 ESP Fit
centers and for floF we have 94,998."

The issue is that Gaussian prints *'s for the fit number after the first
9999 so you have to manually work out how many fit points are there.

Good luck,
Ross

/\
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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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