Re: AMBER: antechamber fails with large molecules

From: Eddie Men <pckboy.gmail.com>
Date: Fri, 02 Nov 2007 02:50:57 -0600

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,
>>> Vânia Calisto
>>>
>>>
>>>
>>>
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Received on Sun Nov 04 2007 - 06:07:37 PST
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