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 - 02:30:02 PDT
