Hi,
Check the .log file after running Step 2. Does it read the variable 'water_model'? If so, I guess the problem is that MCPB.py doesn't actually read "water_model" variable and uses the default option "OPC", which may be a bug. Using an old version of AMBER could solve this problem, such as AMBER18, in which the default option is 'TIP3P' in MCPB.py.
Hope this helps.
Zijian
________________________________
发件人: Jasmin Güven via AMBER <amber.ambermd.org>
发送时间: 2023年3月28日 21:45
收件人: amber.ambermd.org <amber.ambermd.org>
主题: [AMBER] MCPB.py step 2 KeyError with crystal water
Hi,
I'm trying to get force field parameters using MCPB.py for PDB ID 6O5T, which contains two zinc ions (ZN1, ZN2), a water molecule (WAT) and a drug-like small molecule (L8J) in the active site.
I've successfully run my Gaussian DFT calculations for small optimisation, frequency calculation, and the large MK charge calculation. However, when I try to run Step 2, I get the following error:
Traceback (most recent call last):
File "/amber22/bin/MCPB.py", line 667, in <module>
gene_pre_frcmod_file(ionids, premol2fs, stpdbf, stfpf, smresf, prefcdf,
File "/amber22/lib/python3.10/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 think the error is coming from the water molecule, but I have included the mol2 file in my vim2.in file, so I don't know why I am getting this error. Looking at the source code, I think it looks like the code cannot find the mass of water oxygen in the parameter file.
Here's what I have for my vim2.in:
original_pdb vim2_fixed.pdb
group_name vim2
force_field ff14SB
cut_off 2.3
ion_ids 3442 3443
ion_mol2files ZN1.mol2 ZN2.mol2
naa_mol2files L8J.mol2 WAT.mol2
frcmodfiles L8J.frcmod
large_opt 1
gaff 2
water_model TIP3P
software_version g16
Is there something I'm doing wrong in my input? Any help with this would be greatly appreciated!
Kind regards,
J. Jasmin Güven
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.
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Received on Tue Mar 28 2023 - 20:00:02 PDT
