Dear all,
I would appreciate some assistance from anyone who models metal-protein complexes using amber. As you can see from my previous post I've ended up with a warning being thrown whilst executing:
MCPB.py -i my_file.in -s 2
It generates the frcmod files but fails to generate a ..._large_mk.esp. This was the warning:
/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)
I decided to carry on with the hope of understanding what was going on. I went on to execute -s 3 to fit RESP charges. I get the following error:
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/AmberTools21/bin/MCPB.py", line 692, in <module>
resp_fitting(stpdbf, lgpdbf, stfpf, lgfpf, mklogf, ionids, ff_choice,
File "/home/ubuntu/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/pymsmt/mcpb/resp_fitting.py", line 444, in resp_fitting
get_esp_from_gms(mklogf, espf)
File "/home/ubuntu/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/pymsmt/mol/gmsio.py", line 253, in get_esp_from_gms
raise pymsmtError('There is no \'ELECTROSTATIC POTENTIAL\' '
NameError: name 'pymsmtError' is not defined
I assume this is down to the missing .esp file. I believe all of this comes down to an incorrectly resolved GAMESS-US frequency calculation:
https://drive.google.com/drive/folders/1fqzGCACyjZB5L5jaVqC-PYqZETdPtdnZ?usp=sharing
Having always used Gaussian up until last week, I'm struggling to work out whether the output file contains a saddle point, hence complaints about complex numbers in the first error.
Any assistance is hugely appreciated.
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/
________________________________
From: Anthony Nash <anthony.nash.ndcn.ox.ac.uk>
Sent: 09 August 2021 11:46
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] MCPB.py - ComplexWarning: Casting complex values to real discards the imaginary part
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 Wed Aug 11 2021 - 05:00:02 PDT
