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'
> ========================================================================================
>
>
>
>
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--
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/
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Received on Mon Jul 10 2017 - 01:00:03 PDT
