AMBER Archive (2007)

Subject: Re: AMBER: antechamber fails with large molecules

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Nov 02 2007 - 02:24:26 CST

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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