Hi aurora
One more method is that I used openFF charges which is trained on am1bcc
which could work for long polymer chain
On Tue, Jun 23, 2026 at 12:58 PM Arun Srikanth <askforarun.gmail.com> wrote:
> Hi aurora, ideally you can use a long smiles for the polymer chain with
> many repeat units (monomers). Convert that to pdb. Clean the pdb using
> antechamber and calculate the charges using antechamber. The downside of
> this approach is it will take a long time to assign partial charges for the
> whole polymer chain and the monomer charges may not be unique.
> Alternatively you can follow the peg workflow available in the ambet
> tutorials
>
> Hope this helps
>
> Arun
>
> On Tue, 23 Jun 2026, 12:47 Aurora FATIGA via AMBER, <amber.ambermd.org>
> wrote:
>
>> Dear All,
>> My name is Aurora Fatiga, and I am a Ph.D. student at CNR-ITM (based in
>> Rende, Calabria, Italy).
>> I am using AmberTools for my research, specifically AmberTools25.
>>
>> My goal is to create a MOL2 file with gaff2 charges for a polymer chain
>> (PDMS).
>>
>> 1. When using a MOL2 input file and the BCC charge_method, I can generate
>> MOL2 files with GAFF2 charges only for polymers that have a very limited
>> number of repeating units, and I have no problems with either ANTECHAMBER
>> or ACPYPE;
>> 2. The problem occurs for a chain built from a very large number of
>> repeating units (for example, more than 50), so I am forced to use the GAS
>> charge_method; otherwise, it would take a VERY long time to generate my
>> MOL2 file with GAFF2 charges.
>>
>> When I performed these calculations on polymers such as Cellulose-Acetate
>> or Chitosan, I didn't encounter any problems,
>> but for PDMS, the GAS charge_method does not recognize the Si (silicon)
>> atom. It returns this error:
>> .../miniconda3/envs/AmberTools25/bin/wrapped_progs/antechamber: Fatal
>> Error!
>> No Gasteiger parameter for atom (ID: 1, Name: Si, Type: DU).
>>
>> How can I resolve this error? How can I prevent this error?
>>
>> I would like to generalize my question:
>> - I prepare the input MOL2 file using Avogadro, Materials Studio, or
>> other software -
>> Is there a software that allows you to create the MOL2 file for a polymer
>> chain with MANY repeating units in which the gaff2 charges are directly
>> considered, so as to prevent the problem I encountered?
>>
>> I hope I've made myself clear; I look forward to your replies.
>> Best regards,
>> Aurora Fatiga
>>
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>
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Received on Tue Jun 23 2026 - 05:30:02 PDT
