Hello Amber users,
I’m following the Heme-Cys tutorial for MCPB.py
I’m in the step 4 to get the mol2 files for the metal site (HM1.mol2,
CM1.mol2, and FE1.mol2) by:
MCPB.py -i 4ZF6.in -s 3
However, it didn’t work. I addition, I tried to fix this issue
according to this post: http://archive.ambermd.org/201610/0448.html
I obtained the same result.
Here is the output of the command line:
The input file you are using is : 4ZF6.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
The following is the input variable you have:
The variable ion_ids is : [8551]
The variable ion_info is : []
The variable ion_mol2files is : ['FE.mol2']
The variable original_pdb is : tebu_s_complex_H_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']
The variable gaff is : 1
The variable group_name is : tebu_s_complex
The variable ion_paraset is : CM (Only for 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']
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/my_home/software/amber16/bin/MCPB.py", line 684, in <module>
premol2fs, mcresname, 1, chgfix_resids, g0x, lgchg)
File "/home/my_home/software/amber16/lib/python2.7/site-packages/pymsmt/mcpb/resp_fitting.py",
line 468, in resp_fitting
chgs = read_resp_file('resp2.chg')
File "/home/my_home/software/amber16/lib/python2.7/site-packages/pymsmt/mcpb/resp_fitting.py",
line 24, in read_resp_file
chgs.append(float(i))
ValueError: invalid literal for float(): 0.000000********************
Regards,
Aldo
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 12 2017 - 20:00:02 PDT
