AMBER Archive (2006)

Subject: Re: AMBER: respin file

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Sat Nov 25 2006 - 19:07:04 CST

Did you try to use antechamber with the gaussian output file as the input
file to get the resp charges? I think, if you have the second phase of the
gaussian calculation (which is getting the esp data points), you can use
antechamber directly to get the resp charges. Look at page. 80 of AMBER 8
manual (especially example #1). Now, I am assuming that the structure you
are dealing with is just 1 structure (meaning u dont need to do
equivalencing). Hope this helps.

Best,

On Sat, 25 Nov 2006, Fenghui Fan wrote:

> Dear all,
>
> By respgen, I got the follow 2 respin file:
>
> respin1:
> ----------------------
> Resp charges for organic molecule
>
> &cntrl
>
> nmol = 1,
> ihfree = 1,
> ioutopt = 1,
>
> &end
> 1.0
> Resp charges for organic molecule
> 0 0
>
>
>
> -----------------------
>
> respin2:
>
> -----------------------
> Resp charges for organic molecule
>
> &cntrl
>
> nmol = 1,
> ihfree = 1,
> ioutopt = 1,
> iqopt = 2,
> qwt = 0.001,
>
> &end
> 1.0
> Resp charges for organic molecule
> 0 0
>
> -----------------------
>
> Since my original pdb is CYM_ZN and it contains a ZN
> ion. For this reason, will you please tell me how can
> I modify the respin1 and respin2 so that I can use
> resp to get the respout file and the qout file?
>
> As I know, if I use the above mentioned respin1 and
> respin2 without any modification, I cannot get the
> correct qout_stage1.
>
> I am looking forward to getting your reply.
>
> Best regards.
>
> Fenghui Fan
>
>
>
>
>
> ____________________________________________________________________________________
> Cheap talk?
> Check out Yahoo! Messenger's low PC-to-Phone call rates.
> http://voice.yahoo.com
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu