Hi Aldo,
Did you use Gaussian 09 rev B.01 or a different version? If another version, the fix may not be needed.
Kind regards,
Pengfei
> On Jul 13, 2017, at 3:06 PM, Aldo Segura Cabrera <aldoseguracabrera.gmail.com> wrote:
>
> Hi Pengfei,
>
> Thanks for your reply. I did the calculation using gaussian 09 and
> applied the gaussian 09 fix.
>
> Regards,
>
> Aldo
>
> 2017-07-13 14:09 GMT-05:00 Pengfei Li <ambermailpengfei.gmail.com>:
>> 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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>>
>>
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Received on Thu Jul 13 2017 - 13:30:04 PDT
