Hi Abdennour,
It may come from that your total charge was wrong. MCPB.py will calculate the total charge of the system by adding up the charges of all the residues in the metal site (based on the ion and non-amino acid mol2 files you provide and the amino acid mol2 files MCPB.py itself has), if this number is different from the real charge of your metal site, it will cause big error in the RESP charge fitting. I suggest you to check the charges and multiplicities you use for your small model and large model calculations as well as the charge of the metal site MCPB.py assumes.
Kind regards,
Pengfei
> On Jul 10, 2017, at 4:23 AM, liu junjun <ljjlp03.gmail.com> wrote:
>
> From your resp1.out, the charges are very abnormal. Some charges are more
> than 200, and the total charge of entire molecule is -82? There's
> definitely something wrong with your input.
>
> best,
>
> Junjun
>
> On Mon, Jul 10, 2017 at 3:45 PM, abdennour braka <
> abdennour.braka.univ-orleans.fr> wrote:
>
>> Hi,
>> I raise this question.
>> I still can't solve this problem.
>> Could anyone please help me with this?
>> Many thanks
>>
>> Abdennour
>>
>> On 07/07/2017 04:34 PM, abdennour braka wrote:
>>> Dear Amber users,
>>> I follow the tutorial to set up my own system with the heme molecule.
>>> (Http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm)
>>> All the first steps are well done. However, I have a problem when i
>>> perform the RESP charge fitting (MCPB.py -i 3LN0.in -s 3)
>>> It appears that the message comes from a formatting problem of
>>> "resp2.chg". There are also missing values in resp1.pch, resp1.chg (In
>>> attachment)
>>> Any help in this regard is highly appreciated.
>>> Many thanks
>>>
>>> Abdennour
>>>
>>> Here is the output error message
>>>
>>> ******************************************************************
>>> * Welcome to use the MCPB.py program *
>>> * Version 3.0 *
>>> * Author: Pengfei Li *
>>> * Merz Research Group *
>>> * Michigan State University *
>>> * AND *
>>> * Hammes-Schiffer Research Group *
>>> * University of Illinois at Urbana-Champaign *
>>> ******************************************************************
>>> The input file you are using is : 3LN0.in
>>> The following is the input variable you have:
>>> The variable ion_ids is : [8938]
>>> The variable ion_info is : []
>>> The variable ion_mol2files is : ['FE.mol2']
>>> The variable original_pdb is : 3LN0_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', '52B.frcmod']
>>> The variable gaff is : 1
>>> The variable group_name is : 3LN0
>>> The variable ion_paraset is : CM (Only for nonbonded model)
>>> The variable large_opt is : 1
>>> 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', '52B.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/braka/anaconda2/envs/py34/bin/MCPB.py", line 684, in
>>> <module>
>>> premol2fs, mcresname, 1, chgfix_resids, g0x, lgchg)
>>> File
>>> "/home/braka/anaconda2/envs/py34/lib/python3.4/site-
>> packages/pymsmt/mcpb/resp_fitting.py",
>>> line 468, in resp_fitting
>>> chgs = read_resp_file('resp2.chg')
>>> File
>>> "/home/braka/anaconda2/envs/py34/lib/python3.4/site-
>> packages/pymsmt/mcpb/resp_fitting.py",
>>> line 24, in read_resp_file
>>> chgs.append(float(i))
>>> ValueError: could not convert string to float:
>>> '-55.964654165.030579-55.964654-55.964654'
>>> ============================================================
>> ============================
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> --
>> Abdennour BRAKA
>> /PharmD, PhD Student
>> Structural Bioinformatics & Chemoinformatics
>> Institut de Chimie Organique et Analytique (ICOA)
>> UMR CNRS-Université d'Orléans 7311
>> Université d'Orléans
>> Rue de Chartres
>> F-45067 Orléans
>> phone: +33 238 494 577/
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Mon Jul 10 2017 - 19:30:05 PDT
