Hi Aldo,
Which program did you use to do the quantum calculation?
Kind regards,
Pengfei
> On Jul 12, 2017, at 9:47 PM, Aldo Segura Cabrera <aldoseguracabrera.gmail.com> wrote:
>
> 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
>
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Received on Thu Jul 13 2017 - 12:30:03 PDT
