Re: [AMBER] Adding atom types to gaff.dat

From: Pengfei Li <>
Date: Tue, 21 Dec 2021 09:59:29 -0600

Hi Sam,

If you want to develop a new atom type for Ag+ (bonded), you can use the program to handle it once in your original PDB file and the mol2 file for Ag you handle the Ag+ ion correctly. In order to make to recognize the Ag+ ion, you should treat it as an independent residue, and treat both its residue name and atom name as “AG” in both the pdb and mol2 files, and you should treat the atomic charge of the Ag+ ion in its mol2 file as +1.0.

You can check these two tutorials: <> and <>. You can also check the original paper of <>, in its SI there is an example of parameterizing an organometallic compound using A book chapter published in last year provided useful tips for modeling as well.


> On Dec 17, 2021, at 11:50 PM, Sam Walsworth (Researcher) <> wrote:
> Hello
> I'm keen to develop a new atom type for Ag+ (bonded). Can this be done by adding it to the MOD4 section of gaff.dat if I have correct Rmin/2 and epsilon values, or is there issues with this method?
> Sam
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Received on Tue Dec 21 2021 - 08:00:02 PST
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