AMBER Archive (2006)

Subject: Re: AMBER: respin file

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Sat Nov 25 2006 - 21:15:53 CST

You are right.

The thing is that during my ac file preparation, the
antechamber cannot get the correct bond type, thus I
use -j 0. However when I do as you suggets, the prepin
file and the frcmod file are almost empty, that means,
there is nothing related to each atom or each bond.

Followng is my original PDB file:

-------
HEADER Structure from MOLMOL
COMPND CYM_ZN001
ATOM 1 N CYM 33 -2.632 -0.454 0.499
 1.00 0.00
ATOM 2 H CYM 33 -2.424 -0.481 1.487
 1.00 0.00
ATOM 3 CA CYM 33 -1.572 0.022 -0.433
 1.00 0.00
ATOM 4 HA CYM 33 -1.971 0.801 -1.066
 1.00 0.00
ATOM 5 CB CYM 33 -0.391 0.570 0.372
 1.00 0.00
ATOM 6 3HB CYM 33 -0.110 -0.143 1.130
 1.00 0.00
ATOM 7 2HB CYM 33 -0.677 1.500 0.840
 1.00 0.00
ATOM 8 SG CYM 33 1.014 0.862 -0.733
 1.00 0.00
ATOM 9 C CYM 33 -1.104 -1.150 -1.298
 1.00 0.00
ATOM 10 O CYM 33 -0.671 -2.169 -0.798
 1.00 0.00
TER
ATOM 1 Zn Zn 55 2.800 1.527 0.560
 1.00 0.00
TER
END

----------

Will you please tell me the command how can I get the
right gaussian input file (just call it input.ac)? My
way is use -j 0, but it cannot give the correct prepin
and frcmod. But if I delete -j 0, the input.ac cannot
be got by antechamber as the unrecognizable bondtype.

I am looking forward to getting your reply.

Best regards.

Fenghui Fan

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

> 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_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.
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> > > >
> > >
> >
>
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> > > >
> > > >
> > >
> > > --
> > > 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/ -
> > >
> > >
> >
>
---------------------------------------------------------------
> > >
> > >
> >
>
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> >
> >
> >
> >
>
____________________________________________________________________________________
>
=== message truncated ===

 
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