As I wrote in my previous email, polarizable force fields are still under
development. In amber99 force field, there is a parameter defined
as polarizability, but this is for Mg2+ and F- ions. I am not sure how the
polarizability is implemented to AMBER 9, but I am not aware of a fully
constructed polarizable force field. Others might know more about this.
Best,
On Fri, 2 Nov 2007, Eddie Men wrote:
> This is a good question (or one I also have):
>
> "A better solution might be to use a polarizable force field, which will
> change the charges of the atoms by time, depending on the neighbouring
> atoms they are interacting. Polarizable force fields are still in
> development stage, and I am not aware of any fully working polarizable
> force field."
>
> I tried a model with resp charges for ATP braking it into ADP and PO3,
> however when computing free energies the ATP breaks spontaneously at
> very low temperature ( because both molecules are negative charged),
> so I changed to a QM/MM description.
>
> Is it possible to model that reaction with polarizable forece fields?.
> What about mixing force fields?.
>
>
> Eddie
>
>
> Best,
>
>
> Ilyas Yildirim wrote:
> > I know this question was discussed before, but I, also, do not understand
> > the reason to calculate the resp charges for a system like a molecule
> > which has 500 atoms in it. My understanding of charges and its importance
> > in a structure is as follows:
> >
> > Some charge distrubution (point charges in this case) has to be chosen
> > such that it is going to mimic the Q.M. potential around the molecule.
> > Currently, constant charges are used in molecules, meaning the charges
> > do not change by simulation time (except for some polarizable force field
> > implementations, which is still new). The critical question is this: For
> > this molecule, is there only one conformation or more than one? If it is
> > a small molecule, probably it will choose one particular conformation,
> > which implies that one charge distribution might be reasonable enough to
> > mimic the quantum mechanical potential around this molecule.
> >
> > If the structure is too big, then it will probably have more than one
> > conformation to choose. Without knowing the conformations this molecule
> > can choose, a constant charge distribution model will never work. The best
> > thing to do (if someone wants to use constant charge model) is to divide
> > this molecule into sub-molecules (like residues) and then to calculate the
> > charges for these sub-molecules (this is still an approximation though).
> >
> > A better solution might be to use a polarizable force field, which will
> > change the charges of the atoms by time, depending on the neighbouring
> > atoms they are interacting. Polarizable force fields are still in
> > development stage, and I am not aware of any fully working polarizable
> > force field.
> >
> > Best,
> >
> > On Thu, 1 Nov 2007, Junmei Wang wrote:
> >
> >
> >> Personally I don't think there is a good approach to get good charges (such as HF/6-31G* RESP). AM1BCC may be a good candidate. The problem is that antechamber may not handle such large molecules well. In amber10, I have improved the code a little bit to handle large molecules much better, in a long run I also plan to develop a even simpler, but more reliable charges (compared to am1-bcc) for arbitrary organic molecules. This method will be available in amber11.
> >>
> >> Best
> >>
> >> Junmei
> >>
> >> ----- Original Message ----
> >> From: Francesco Pietra <chiendarret.yahoo.com>
> >> To: amber.scripps.edu
> >> Sent: Thursday, November 1, 2007 3:29:26 AM
> >> Subject: Re: AMBER: antechamber fails with large molecules
> >>
> >> You may remeber that I tried unsuccessfully to get the partial charges with
> >> Antechamber in Amber9 for a 500-atoms non-repetitive molecule. Prof Case, and
> >> others, suggested, however, that, even if calculated, the partial charges would
> >> be unreliable for such a large residue.
> >>
> >> Is the new code intended to solve this question too?
> >>
> >> At any event, do you plan to make the new code available? An when? I have
> >> frequently problems of large ligands.
> >>
> >> Thanks
> >>
> >> francesco pietra
> >>
> >>
> >> --- Junmei Wang <junmwang.yahoo.com> wrote:
> >>
> >>
> >>> Could you send me the file? I have modified the respgen.c code a little bit
> >>> to handle large molecules, but it is not in amber9.
> >>>
> >>> Best
> >>>
> >>> Junmei
> >>>
> >>> Dear amber users:
> >>>
> >>> I am trying fit RESP charges with antechamber to a large
> >>> organic molecule (342 atoms) with the command:
> >>>
> >>> antechamber –i biscalix.log –fi gout –o biscalix_resp.mol2
> >>> -fo mol2 –c resp
> >>>
> >>> This fitting process failed with the following errors:
> >>>
> >>> “The number of the path atoms exceeds
> >>> MAXPATHATOMNUM(1900000) for atom[148],extend the size and
> >>> reallocate the memory automatically reallocate memory for
> >>> pathscore[148] failed
> >>> Info: the atom number exceeds the MAXATOM, reallocate
> >>> memory automatically
> >>> Amber 9 RESP
> >>> Unit 5 Error on OPEN: ANTECHAMBER_RESP1.IN
> >>> Error: cannot run "resp -O -i ANTECHAMBER_RESP1.IN -o
> >>> ANTECHAMBER_RESP1.OUT -e ANTECHAMBER.ESP -t qout" in
> >>> resp() of charge.c properly, exit”.
> >>>
> >>> Could someone give me any idea about how to solve this
> >>> type of problems?
> >>>
> >>> Thanks in advance,
> >>> Vānia Calisto
> >>>
> >>>
> >>>
> >>>
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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 Sun Nov 04 2007 - 06:07:38 PST
