In these papers, they deal with POPC molecule and calculate the resp
charges for POPC so that they can form a 128 POPC bilayer structure. They
choose 12 conformations for POPC and they show that with this choice, they
can predict some of the experimental results. Whether 12 is enough or not,
I do not know. I am sure they have their reasons on why they have chosen
12 conformations for POPC.
It is, still, following the resp protocol, though I am not sure how they
followed the resp protocol. POPC looks more complicated than an RNA
nucleotide, but it is still possible to follow the resp protocol to
calculate the charges. After the resp charge calculation for POPC, they
create the molecule which has 128 POPC in it.
So, for a 500 atom system, can you calculate the resp charges? Quantum
Mechanical optimization can take forever for this system. If you want to
stick with fixed charge method, you have to divide your structure into sub
structures. Dr. SantaLucia's group created a database for modified RNA
nucleotides.
http://ozone3.chem.wayne.edu:8080/Modifieds/jsps/move.jsp#
In their paper (Aduri, R., Psciuk, B. T., Saro, P., Taniga, H., Schlegel,
H. B., SantaLucia, J., Jr. (2007) "AMBER Force Field Parameters for the
Naturally Occurring Modified Nucleosides in RNA", J. Chem. Theory and
Comput., 3, 1464 -1475.), they explain how they calculated the resp
charges. For some big complicated nucleotides, they made some
approximations such as diving that particular nucleotide into 2 parts; one
is the sugar part and the other one is the base part. They optimize and
calculate the resp charges of these two parts seperately. At the end, they
combine these two parts to create the library file for that particular
complicate nucleotide.
So, even though you cannot calculate the resp charges for a 500 atom
system directly, you can make approximation by diving the structure into
small segments and calculate the resp charges for those segments
seperately. At the end, you can combine the resp charges to create your
library file for 500 atom system. How to divide your structure into
sub segments/structures depend on how your structure looks like. The most
important point of these sub segments should be that they should not
interact with each other crucially (at least the interaction should not be
too big). For instance, in an RNA nucleotide, you can divide the
nucleotide into sugar + base because the interaction between these two is
not too big (at least that is what the approximation is in some of the
resp calculations in the above database).
By the way, when you use antechamber to get the charges, they won't be
the resp charges.
Best,
On Fri, 2 Nov 2007, Francesco Pietra wrote:
> 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.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.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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> > > >>
> > > >>
> > > >>
> > > >> __________________________________________________
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> > > >
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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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>
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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 - 06:07:54 PST
