Dear Edo,
How about creating this 3CYG-CU complex, and find the resp charges of each
atom after optimizing the geometry? Then, you can create 3 new residues,
CY1/CY2/CY3 and use them in your structure. In the resp procedure, I
would suggest you to ensure that the charges of C and N terminal atoms to
be conserved with the currently defined charges, so that the joint points
have the same charges.
Good luck,
PS: I never saw it before, but I am curious if this is possible: Is it
possible to create a complex/structure/residue, such that someone can
define more than 2 terminals to it? In nucleic acids, you have the 3'/5'
ends. Is it possible to define another end in AMBER?
On Tue, 25 Sep 2007 saccenti.cerm.unifi.it wrote:
> Hi Steve,
>
> I indeed found out this solution: in CYM the net charge is -1
> I can prepare a CU(I) prep file with charge +1 so that the total charge
> is -1x3 + 1 = -2.
>
> I'm pretty new to this, but I have been warned that charges must be
> distribuited over all the atoms of the complex:
>
>
> (-1)CYG CYG(-1)
> \Cu(+1)/
> |
> CYC(-1)
>
> I do not know if this is correct
>
> The parameters I was using comes from CYG-Cu-CYG and in that case the sum
> over the Cu and CYG charges is indeed -1
>
> For the moment I'm using the same approach you kindly suggested but I'm
> also looking for some reliable information about charge redistribution in
> a such system with 3 cysteines and a copper(I)
>
> Any more details or suggestion is more than welcome
>
> Greets
> Edo
>
> > Hi Edo,
> >
> > I don't know if this would be appropriate for your system, but at least
> > it's
> > worth checking out.
> >
> > Parameters for an anionic cysteine have already been determined according
> > to
> > the descriptions of most force fields and are actually already built into
> > the residue libraries for most of the Amber force fields. The residue
> > name
> > is CYM. If you simply change the names of the residues in your PDB file
> > from CYG to CYM, leap will read the built-in parameters and you don't even
> > need the CYG prep file.
> >
> > Steve
> >
> >
> > -----Original Message-----
> > From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> > Of
> > Ilyas Yildirim
> > Sent: Monday, September 24, 2007 5:54 PM
> > To: amber.scripps.edu
> > Subject: Re: AMBER: Help WARNING: The unperturbed charge of the unit
> >
> > Dear Edo,
> >
> > You have created a new CYG residue and new charge parameter for CU atom.
> > The new CYG residue has a total charge of -0.698, and CU is 0.396. In
> > your inpdb file, you have 3 CYG, and 1 CU, and when you add them up, the
> > total charge of the system is -1.698000.
> >
> > Where did you get these parameters? Also, do you know what the total
> > charge of your structure is? The new CYG residue - I guess - should
> > have a -1 charge (The title of the CYG_prep is 'CYSTEINE with negative
> > charge'). You might want to follow the resp procol to calculate the
> > resp charges for your new CYG residue.
> >
> > I cant say too much about your system, or what to do with the 3 CYG - Cu
> > region, but the reason why you see noninteger number is due to the charges
> > defined for CYG and CU.
> >
> > Good luck,
> >
> > On Mon, 24 Sep 2007 saccenti.cerm.unifi.it wrote:
> >
> >> Dear All,
> >> I'm getting the following
> >>
> >> Checking Unit.
> >> WARNING: There is a bond of 3.363639 angstroms between:
> >> ------- .R<CYG 87>.A<SG 8> and .R<CU 148>.A<CU 1>
> >> ERROR: The unperturbed charge of the unit: -1.698000 is not integral.
> >> WARNING: The unperturbed charge of the unit: -1.698000 is not zero.
> >>
> >> -- ignoring the error and warnings.
> >>
> >> I'm aware that the total charge must be equal to zero
> >> and also think that this must depend or on CGY or Cu or on both.
> >>
> >> I browsed the amber archive and tried several suggestion, but I'm still
> >> getting that error
> >>
> >> Does somebody as some idea on how to fix this bug?
> >> I attach the files I'm using
> >>
> >> Many thanks
> >> edo
> >>
> >>
> >
> > --
> > Ilyas Yildirim
> > ---------------------------------------------------------------
> > = Department of Chemistry - =
> > = University of Rochester - =
> > = Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
> > = http://www.pas.rochester.edu/~yildirim/ =
> > ---------------------------------------------------------------
> >
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>
>
>
--
Ilyas Yildirim
---------------------------------------------------------------
= Department of Chemistry - =
= University of Rochester - =
= Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
= http://www.pas.rochester.edu/~yildirim/ =
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Received on Wed Sep 26 2007 - 06:07:22 PDT
