Dear all,
I'm working my way through the MCPB.py workflow for a protein with 6 metal ions.
Five of those six metals are working, however, whilst executing MCPB.py MMP1_ca_1104.in -s 2 I notice two "ComplexWarning" in the output to the screen (error below).
My input files is:
original_pdb corrected_ca_1104.pdb
group_name MMP1_ca_1104
cut_off 2.8
ion_ids 5808
ion_mol2files calcium_atom_1104.mol2
large_opt 1
force_field ff99SB
software_version gms
Until recently, I had been using Gaussian. Now, without a license, I am using GAMESS-US for the first time. I believe, there are no imaginary frequencies in the output (file in the link below). However, the error from MCPB.py makes me feel like there should be.
I would appreciate some assistance with this issue.
GAMESS-US FREQ FILE:
https://drive.google.com/drive/folders/1fqzGCACyjZB5L5jaVqC-PYqZETdPtdnZ?usp=sharing
MCPB.PY COMPLEX WARNING:
For angletype: Y5-M1-Y6. There are 1 angle(s) in this type:
The angle value(s) is(are): [97.48]
The average angle value is: 97.48 Degree.
The force constant(s) is(are): [46.55]
The average force constant is: 46.55 Kcal*mol^-1*Rad^-2.
/home/ubuntu/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/pymsmt/mcpb/gene_final_frcmod_file.py:168: ComplexWarning: Casting complex values to real discards the imaginary part
print('%5s %5.1f %7.4f %-s' %(bondtyp, param[0], param[1], note), file=finfrcmod)
/home/ubuntu/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/pymsmt/mcpb/gene_final_frcmod_file.py:161: ComplexWarning: Casting complex values to real discards the imaginary part
print('%8s %7.2f %7.2f %-s' %(angtyp,param[0], param[1], note), file=finfrcmod)
==================================================================
To cite MCPB.py please use the following reference:
Pengfei Li and Kenneth M. Merz, Jr., "MCPB.py: A Python Based
Metal Center Parameter Builder", J. Chem. Inf. Model., 2016,
56, 599-604.
Helpful tips can be found in the following book chapter:
Pengfei Li and Kenneth M. Merz, Jr., "Parameterization of a Dioxygen
Binding Metal Site Using the MCPB.py Program", Methods Mol. Biol.,
2021, 2199, 257-275.
<
https://drive.google.com/drive/folders/1fqzGCACyjZB5L5jaVqC-PYqZETdPtdnZ?usp=sharing>Many thanks
Anthony
Kind regards
Dr Anthony Nash PhD MRSC
Senior Research Scientist
Nuffield Department of Clinical Neurosciences
RMCR Kellogg College
University of Oxford
http://www.kellogg.ox.ac.uk/
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Received on Mon Aug 09 2021 - 04:00:02 PDT
