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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Received on Thu Jul 13 2017 - 13:30:04 PDT
