I guess you are confusing yourself with the definitions. Let me explain a
little bit more on what I tried to say in my previous email.
1. You have a structure. Let us call it as x.pdb.
2. You use an ab initio program (like gaussian) to optimize the structure.
3. You use an ab initio program (again) to get the ESP data points (PS:
The 2nd and 3rd steps can be combined. If you have created the gaussian
input file for your structure x.pdb using antechamber, this is the case).
4. After finishing the second phase of the gaussian calculation (which is
getting the ESP Data points), u use antechamber to get the resp charges.
When u use antechamber, it will do all the steps automatically.
As I said before, I assume that u are trying to get the resp charges for
just 1 structure (meaning u dont need to deal with equivalencing). Hope
this helps.
Best,
On Sat, 25 Nov 2006, Fenghui Fan wrote:
> 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.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.scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to
> > majordomo.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.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to
> > majordomo.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.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.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.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Nov 26 2006 - 06:07:42 PST
