AMBER Archive (2006)

Subject: Re: AMBER: respin file

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Sat Nov 25 2006 - 19:49:58 CST

Thank you very much.

First I get the gaussian output file, then I use the
gaussian output file to get the esp file, the I start
to get the resp charge, but I cannot get the qout.

I will refer to your e-mail and try to make it
workable. If you have any comments, please tell me.

Best regards.

Fenghui Fan

--- Ilyas Yildirim <yildirim_at_pas.rochester.edu> wrote:

> 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
>

 
____________________________________________________________________________________
Do you Yahoo!?
Everyone is raving about the all-new Yahoo! Mail beta.
http://new.mail.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