[AMBER] MCPB, Unrecognized OW type for water

From: Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org>
Date: Sun, 3 Dec 2023 09:22:37 -0600

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 - 07:30:03 PST
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