Hi Matthew,
This issue may be because the separation of the water model from the protein force field in the most recent versions of AmberTools, in this way MCPB.py could not find the water model parameters from the protein force field. The MCPB.py program in the future release (i.e. AmberTools24) will have this issue fixed.
To solve this problem now, (I assume you are using the opc water model, if you are using another water model, you can adjust accordingly) you can copy the $AMBERHOME/dat/leap/parm/frcmod.opc file into your working folder, and then add "frcmod_files frcmod.opc” into your MCPB.py input file and do the MCPB.py procedure from the beginning.
Hope it helps,
Pengfei
> On Dec 3, 2023, at 9:19 AM, Matthew Guberman-Pfeffer <mgubermanpfeffer.icloud.com> wrote:
>
> 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 Tue Dec 05 2023 - 15:00:03 PST
