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 - 05:00:04 PDT
