AMBER Archive (2006)

Subject: Re: AMBER: respin file

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Sun Nov 26 2006 - 11:12:01 CST

Than you very much for your reply.

As for the CYM.pdb structure mentioned in your
protocol, it should be not be neutral, because it
lacks the H in the SH and one H in the N-terminal NH2.

Somebody treat the bond between the SG of CYM and the
ZN as a covalent bond. I have tried this way, the
situation is that the prepin file of the CYM-ZN.pdb
lackes the information of the ZN and the last two
atoms (I think the last 2 atoms should be ZN), thus in
the frcmod file, there is no information on the ZN
related bonds.

For your protocol, if we treat ZN separately, that
means we will have a PDB contains the coordinates of
only ZN, then we can get the ZN library file, but how
about its prepin file and the its frcmod file?

The other question is about the command you mentioned:

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

What will be the charge type of this command?

I am looking forward to getting your reply.

Best regards.

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

> 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
>
=== message truncated ===

 
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