Dear All,
I'm trying to parameterize heme using MCPB.py tool and this tutorial.
I've used this tool successfully in the past, but the 2HI4 structure is
giving errors, and the tool needs to recognize the metal correctly.
It is being treated as F ion, not Fe.
There was a floating error in step 3 when I fixed the G16 input files
manually and ran step 2.
I've attached the prepared protein, frcmod file and MCPB.py input file.
I have tried with amber18, 22 and 24, but all give the same error.
Any suggestions and tips to solve the issue would be appreciated.
(base) [vaibhav.param_embryo MD-simulations-CYP1A2]$ MCPB.py -i 2hi4-mcbp.in
-s 3
******************************************************************
* Welcome to use the MCPB.py program *
* Version 2024 *
* Author: Pengfei Li *
* Merz Research Group *
* Michigan State University *
* AND *
* Hammes-Schiffer Research Group *
* Yale University *
* AND *
* Li Research Group *
* Loyola University Chicago *
******************************************************************
The input file you are using is : 2hi4-mcbp.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
The following is the input variable you have:
The variable ion_ids is : [7810]
The variable ion_info is : []
The variable ion_mol2files is : ['FE.mol2']
The variable original_pdb is : 2hi4-Hplus-merged-renum.pdb
The variable add_bonded_pairs is : []
The variable add_redcrd is : 0
The variable additional_resids is : []
The variable anglefc_avg is : 0
The variable bondfc_avg is : 0
The variable chgfix_resids is : []
The variable cut_off is : 2.8
The variable force_field is : ff14SB
The variable frcmod_files is : ['HEM.frcmod', 'ligand.frcmod']
The variable gaff is : 1
The variable group_name is : 2HI4
The variable ion_paraset is : 12_6 (Only for the ions using the nonbonded
model).
The variable large_opt is : 0
The variable lgmodel_chg is : -99
The variable lgmodel_spin is : -99
-99 means program will assign a charge automatically.
The variable naa_mol2files is : ['HEM.mol2', 'ligand.mol2']
The variable scale_factor is : 1.0
ATTENTION: This is the scale factor of frequency. The
force constants will be scaled by multiplying the square
of scale_factor.
The variable smmodel_chg is : -99
The variable smmodel_spin is : -99
-99 means program will assign a charge automatically.
The variable software_version is : g09
The variable sqm_opt is : 0
The variable water_model is : TIP3P
The variable xstru is : 0
******************************************************************
* *
*======================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...
Traceback (most recent call last):
File "/home/software/amber24/bin/MCPB.py", line 707, in <module>
resp_fitting(stpdbf, lgpdbf, stfpf, lgfpf, mklogf, ionids, ff_choice,
File
"/home/software/amber24/lib/python3.12/site-packages/pymsmt/mcpb/resp_fitting.py",
line 469, in resp_fitting
chgs = read_resp_file('resp2.chg')
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/software/amber24/lib/python3.12/site-packages/pymsmt/mcpb/resp_fitting.py",
line 24, in read_resp_file
chgs.append(float(i))
^^^^^^^^
ValueError: could not convert string to float: '7.332771-10.051991'
Thank you and best regards,
Regards,
Dr. Vaibhav A. Dixit,
Asst. Prof., Department of Medicinal Chemistry,
National Institute of Pharmaceutical Education and Research, Guwahati
(NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
781101, Assam, India
Mob. No. +91-7709129400,
Email: vaibhav.niperguwahati.in; vaibhavadixit.gmail.com
https://niperguwahati.ac.in/DOC/profile/dixit.pdf
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
NCBI bibliography:
https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Wed Jul 17 2024 - 23:00:02 PDT
