Thanks for your reply. Attached are all my input files that gives the problem with the water ligand.

> On Dec 3, 2023, at 9:56 AM, 郭 家藩 via AMBER <amber.ambermd.org> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> Hi,
> In old MCPB tutotial, the ligated water molecule is treated as a hydroxyl group. If you want more help, you should provide inputs file for reference.
> ________________________________
> 发件人: Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org <mailto:amber.ambermd.org>>
> 发送时间: 2023年12月3日 23:22
> 收件人: AMBER Mailing List <amber.ambermd.org <mailto:amber.ambermd.org>>
> 主题: [AMBER] MCPB, Unrecognized OW type for water
>
> Dear Amber Community,
>
> I’m trying to parameterize a Zn site with MCPB similar to the tutorial <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial20%2Fmcpbpy.php&data=05%7C01%7Cmatthew.guberman-pfeffer%40uconn.edu%7C66c84e2ece44411f5e2508dbf4187da5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C638372158254176669%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Dya7VymzO17a7zveeE5UWa3iux%2BgQNgc4t0rIuRU4pY%3D&reserved=0>, except there is a ligated water molecule and no non-standard organic ligand. When I run step 2 of MCPB, it complains that it does not recognize atom type OW:
>
> 967-WAT.15372-O : OW --> Y3
> Traceback (most recent call last):
> File "/usr/local/amber22/bin/MCPB.py", line 665, in <module>
> gene_pre_frcmod_file(ionids, premol2fs, stpdbf, stfpf, smresf, prefcdf,
> File "/usr/local/amber22/lib/python3.9/site-packages/pymsmt/mcpb/gene_pre_frcmod_file.py", line 132, in gene_pre_frcmod_file
> print('YES', atyp2 + massparms[atyp1], file=fmf)
> KeyError: 'OW'
>
> I included in the input file:
>
> naa_mol2files WAT.mol2
> water_model TIP3P
>
> Where the mol2 was generate as instructed in the tutorial.
>
> What am I doing wrong?
>
> Best,
> Matthew
>
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Received on Sun Dec 03 2023 - 09:00:02 PST
