Dear Amber experts and Pengfei Li,
I'm getting the following error message at step 3 of the MCPB.py procedure
for a FeS protein.
The gaussian jobs finished correctly but I'm getting this error message.
Please suggest what might be the cause for this error and if a patch is
available to fix the same.
Thank you and best regards.
(base) [vaibhav.param_embryo dir]$ MCPB.py -i mcpb.in -s 3
******************************************************************
* Welcome to use the MCPB.py program *
* Version 7.0 *
* 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 : 2v3b-mcpb.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
The following is the input variable you have:
The variable ion_ids is : [809]
The variable ion_info is : []
The variable ion_mol2files is : ['FE.mol2']
The variable original_pdb is : 2v3b-B-3.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 : ff19SB
The variable frcmod_files is : []
The variable gaff is : 1
The variable group_name is : 2V3B
The variable ion_paraset is : 12_6 (Only for the ions using the nonbonded
model).
The variable large_opt is : 1
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 : []
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 : OPC
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/amber22/bin/MCPB.py", line 692, in <module>
resp_fitting(stpdbf, lgpdbf, stfpf, lgfpf, mklogf, ionids, ff_choice,
File
"/home/software/amber22/lib/python3.9/site-packages/pymsmt/mcpb/resp_fitting.py",
line 469, in resp_fitting
chgs = read_resp_file('resp2.chg')
File
"/home/software/amber22/lib/python3.9/site-packages/pymsmt/mcpb/resp_fitting.py",
line 24, in read_resp_file
chgs.append(float(i))
ValueError: could not convert string to float: '4.515688-13.332407'
(base) [vaibhav.param_embryo 2V3B-FMN-ox-Fe2]$
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Oct 01 2022 - 23:00:03 PDT
