Hi Sam,
If you want to develop a new atom type for Ag+ (bonded), you can use the MCPB.py 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 MCPB.py 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: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm> and http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm>. You can also check the original paper of MCPB.py: https://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00674 <https://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00674>, in its SI there is an example of parameterizing an organometallic compound using MCPB.py. A book chapter published in last year provided useful tips for MCPB.py modeling as well.
Pengfei
> On Dec 17, 2021, at 11:50 PM, Sam Walsworth (Researcher) <Sam.Walsworth.hud.ac.uk> 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
