AMBER Archive (2006)

Subject: Re: AMBER: respin file

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Sun Nov 26 2006 - 02:03:33 CST

The .pdb file u have attached have 2 unique residues, one is called CYM
and the other one is Zn. What u have to do is erase the Zn residue, and
save the file (for example, as CYM.pdb). Then,

antechamber -i CYM.pdb -fi pdb -o cym.in -fo gcrt

This will create a file 'cym.in', which is a gaussian input file. It will
do both the gaussian optimization + MEP calculation (aka ESP data point
calculation). After finishing this gaussian calculation, u can -again- use
antechamber to create (for instance) a .mol2 file, which will let u load
this structure into LeAP.

For the Zn, u need to use other parameters (if there are any parameter
set defined for Zn). In this protocol, I assumed that the structure
CYM.pdb is neutral. If it is not, u have to modify cym.in file (For more
information on how to do it, check out the gaussian manual, which can be
found at http://www.gaussian.com/g_ur/g03mantop.htm - this is a very
useful online manual if u use gaussian often).

You might use the program R.E.D. II for this resp charge calculation. For
more information on R.E.D., check out the following website:

http://www.u-picardie.fr/labo/lbpd/RED/

Best,

PS: I might be missing something here. I assumed that u are trying to find
the resp charges. The above explanation is to find the resp charges. After
getting these charges for CYM.pdb atoms, u can use antechamber and create
a .mol2 file, which will have the atom type info in it.

On Sat, 25 Nov 2006, Fenghui Fan wrote:

> 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
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > >
> >
> ____________________________________________________________________________________
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> > > >
> > > > --
> > > > Ilyas Yildirim
> > > >
> > > >
> > >
> >
> ---------------------------------------------------------------
> > > > - Department of Chemisty - -
> > > > - University of Rochester - -
> > > > - Hutchison Hall, # B10 - -
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> > 67
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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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