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>
发送时间: 2023年12月3日 23:22
收件人: AMBER Mailing List <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://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 Sun Dec 03 2023 - 08:00:02 PST
