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 - 13:30:03 PDT
