Dear all,
This is related to my earlier email "MCPB.py - ComplexWarning...", which I moved past onto the 3rd stage of MCPB.py, the assigning of RESP charges.
For clarity, everything has worked up until I tried working on the 6th metal site in my protein.
I am seeing the following error:
******************************************************************
* *
*======================RESP Charge fitting=======================*
* *
******************************************************************
***Generating the 1st stage resp charge fitting input file...
***Generating the 2nd stage resp charge fitting input file...
***Doing the RESP charge fiting...
MMP1_ca_1104_large_mk.esp
CAUTION: THE VDW RADIUS OF ATOMIC NUMBER 20IS UNKNOWN AND HAS BEEN SET TO1.80 ANGSTROMS IN THE GAMESS CALCULATION.
Unit 3 Error on OPEN: resp1.chg
OR HERE...
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 472, in resp_fitting
chgs = read_resp_file('resp2.chg')
File "/home/ubuntu/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/pymsmt/mcpb/resp_fitting.py", line 18, in read_resp_file
fp = open(fname, 'r')
FileNotFoundError: [Errno 2] No such file or directory: 'resp2.chg'
Digging around, the code in resp_fitting.py executes:
resp -O -i resp1.in -o respl1.out -p resp1.pch -t resp1.chg -e MMP1_ca_1104_mk_large.esp -s resp1_calc.esp
This does not produce the resp1.chg file, so further calculations cause the script to crash.
This is my input:
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
I'm now pushing hard against a fast-approaching manuscript resubmission. Any suggestions are massively 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/
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Received on Mon Aug 16 2021 - 04:00:02 PDT
