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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Received on Tue Jun 23 2026 - 05:00:05 PDT
