AMBER Archive (2007)

Subject: Re: AMBER: antechamber fails with large molecules

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri Nov 02 2007 - 11:07:52 CST

Hopefully polarizable force fields will put - they alone - the house in order.
I doubt, simply because it seems too good.

People using the fixed charge strategy have long devised to mediate between
conformers. A very careful piece of work to this regard came recently from
Hungary, concerning the POPC lipidic double layer (J Comput Chem 2007, 28,
2051-8). Is such type of huge work absolutely needed routinely? Other groups -
in the context of hugh-level publication - still treat the same POPC with fixed
charges for a single conformer (JACS 2007, 129, 6970-1). Surely, it depends on
the precision to attain. My conformers, plagued by huge degrees of freedom and
differing in energy by 1 kcal/mol, can't be treated computationally in
condensed phase at any level of theory.

francesco

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

> 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_at_yahoo.com>
> > >> To: amber_at_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_at_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,
> > >>> Vânia 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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