I check you files and try to use build system by MCPB. I think changing the name of water in tutorial is aim to save the crystal water during operation. In MCPB model, It is theorized that water located at the center of metalloenzyme activity is involved in nucleophilic reactions. If the water molecule is also involved in the catalytic reaction in your system, you should remove a hydrogen atom from the water molecule and modify the atom name and residue name to treat it as a ligand. In other words, It is not a intact water molecule but a OH- group.
________________________________
发件人: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
发送时间: 2023年12月4日 0:53
收件人: 郭 家藩 <guoyingfan.outlook.com>; AMBER Mailing List <amber.ambermd.org>
主题: Re: [AMBER] MCPB, Unrecognized OW type for water
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<
https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.php>>, 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 Tue Dec 05 2023 - 01:00:02 PST
