Hi Aldo,
Good to know that!
Kind regards,
Pengfei
> On Jul 13, 2017, at 3:16 PM, Aldo Segura Cabrera <aldoseguracabrera.gmail.com> wrote:
>
> Hi Pengfei,
>
> You're right! I have a different version.
>
> I did it again without the fix and it works!
>
> Thanks,
>
> Aldo
>
> 2017-07-13 15:10 GMT-05:00 Pengfei Li <ambermailpengfei.gmail.com>:
>> 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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>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
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Received on Fri Jul 14 2017 - 14:00:02 PDT
