Hi Aashish,
Which version of Gaussian did you use?
Pengfei
> On Jan 26, 2018, at 12:47 AM, Aashish Bhatt <aashish.ph16221.inst.ac.in> wrote:
>
> Dear Sir
>
> I have already supplied large mk.log file but again showing error.
> and resp is working when i used in via command line.
>
> sir can i use respgen for resp charge fitting?
> http://ambermd.org/antechamber/ac.html#respgen <http://ambermd.org/antechamber/ac.html#respgen>
>
>
>
> On Fri, Jan 26, 2018 at 12:04 AM, Pengfei Li <ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>> wrote:
> Hi Aashish,
>
> This problem is weird. Did you have the large_mk.log file in that directory? Do you have resp program correctly installed in your computer?
>
> Pengfei
>
> > On Jan 22, 2018, at 5:33 AM, Aashish Bhatt <aashish.ph16221.inst.ac.in <mailto:aashish.ph16221.inst.ac.in>> wrote:
> >
> > Dear Sir
> >
> > I have change name from HEM to FE in PDB file. now its working.
> > but i am getting error in 3rd step MCPB.py -i mcpb_3rd.in <http://mcpb_3rd.in/> -s 3
> >
> > IOError: [Errno 2]no such file or directory: 'resp2.chg'
> >
> > I have searched on amber forum but this error is not answered .
> >
> > Regards
> > Aashish Bhatt
> >
> >
> > On Wed, Jan 17, 2018 at 1:37 AM, Pengfei Li <ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com> <mailto:ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>>>
> > wrote:
> >
> >> Hi Aashish,
> >>
> >> Do you have the FE.mol2 file exactly equal to the FE.mol2 file in this
> >> tutorial: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm> <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm>>
> >> <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm> <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm>>>? That
> >> could be the reason.
> >>
> >> Kind regards,
> >> Pengfei
> >>
> >>> On Jan 8, 2018, at 10:47 PM, Aashish Bhatt <aashish.ph16221.inst.ac.in <mailto:aashish.ph16221.inst.ac.in> <mailto:aashish.ph16221.inst.ac.in <mailto:aashish.ph16221.inst.ac.in>>>
> >> wrote:
> >>>
> >>> Dear Sir
> >>>
> >>> I am preparing force field parameter of HEME so I am following the
> >> tutorial
> >>> (*http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm> <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm>>
> >>> <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm> <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm>>>)*
> >> and I
> >>> have found the KeyError: 'FE' .All the required files are created but
> >>> file_small.res is empty.,so am unable to understand the results and the
> >>> error in my calculations if any . I will be highly grateful if you could
> >>> help me reading the error attached below .
> >>>
> >>> $ MCPB.py -i 4lod.in <http://4lod.in/> -s 1
> >>>
> >>> ******************************************************************
> >>> * Welcome to use the MCPB.py program *
> >>> * Version 2.0 *
> >>> * Author: Pengfei Li *
> >>> * Merz Research Group *
> >>> * Michigan State University *
> >>> ******************************************************************
> >>> The input file you are using is : 4lod.in <http://4lod.in/>
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> >>> The following is the input variable you have:
> >>> The variable ion_ids is : [23399]
> >>> The variable ion_info is : []
> >>> The variable ion_mol2files is : ['FE.mol2']
> >>> The variable original_pdb is : 4lod_add_H.pdb
> >>> The variable add_bonded_pairs is : []
> >>> The variable additional_resids is : []
> >>> The variable anglefc_avg is : 0
> >>> The variable bondfc_avg is : 0
> >>> The variable cut_off is : 2.8
> >>> The variable chgfix_resids is : []
> >>> The variable force_field is : ff14SB
> >>> The variable frcmodfs is : ['HEM.frcmod']
> >>> The variable gaff is : 1
> >>> The variable group_name is : 4lod
> >>> The variable ion_paraset is : CM (Only for nonbonded model)
> >>> The variable large_opt is : 0
> >>> The variable lgmodel_chg 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
> >>> -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
> >>> ******************************************************************
> >>> * *
> >>> *=======================Metal Site Information===================*
> >>> * *
> >>> ******************************************************************
> >>> ***Selected Metal ion FE is atom 23399 in residue 1495-HEM
> >>> 12-CYS.SG is in 2.8 Angstrom of or set bonded (in the input file) to
> >> (one
> >>> of) these metal ions
> >>> 25-HIE.NE2 is in 2.8 Angstrom of or set bonded (in the input file) to
> >> (one
> >>> of) these metal ions
> >>> 1494-HEM.NA is in 2.8 Angstrom of or set bonded (in the input file) to
> >> (one
> >>> of) these metal ions
> >>> 1494-HEM.NB is in 2.8 Angstrom of or set bonded (in the input file) to
> >> (one
> >>> of) these metal ions
> >>> 1494-HEM.NC is in 2.8 Angstrom of or set bonded (in the input file) to
> >> (one
> >>> of) these metal ions
> >>> 1494-HEM.ND is in 2.8 Angstrom of or set bonded (in the input file) to
> >> (one
> >>> of) these metal ions
> >>> ***The following residues are in the Metal Site:
> >>> Residue 12-CYS
> >>> Residue 25-HIE
> >>> Residue 1494-HEM
> >>> Residue 1495-HEM
> >>> ***The small model contains the following residues:
> >>> [12, 25, 1494, 1495]
> >>> ***The large model contains the following residues:
> >>> [11, 12, 13, 24, 25, 26, 1494, 1495]
> >>> ******************************************************************
> >>> * *
> >>> *=======================Building models==========================*
> >>> * *
> >>> ******************************************************************
> >>> ***Creating the small model...
> >>> It contains the residue 12-CYS as sidechain coordinated.
> >>> It contains the residue 25-HIE as sidechain coordinated.
> >>> It contains the residue 1494-HEM as normal.
> >>> It contains the residue 1495-HEM as normal.
> >>> Totally there are 97 atoms in the small model.
> >>> Totally there are 389 electrons in the small model.
> >>> ***Creating the standard model...
> >>> It contains the residue 12-CYS as normal.
> >>> It contains the residue 25-HIE as normal.
> >>> It contains the residue 1494-HEM as normal.
> >>> It contains the residue 1495-HEM as normal.
> >>> Totally there are 101 atoms in the standard model.
> >>> ***Creating the large model...
> >>> Creating the residue 11-ARG into ACE...
> >>> It contains the residue 12-CYS as normal.
> >>> Creating the residue 13-THR into NME...
> >>> Creating the residue 24-PRO into ACE...
> >>> It contains the residue 25-HIE as normal.
> >>> Creating the residue 26-HIE into NME...
> >>> It contains the residue 1494-HEM as normal.
> >>> It contains the residue 1495-HEM as normal.
> >>> Totally there are 125 atoms in the large model.
> >>> Totally there are 509 electrons in the large model.
> >>> Traceback (most recent call last):
> >>> File "/home/ehesan/Software/amber16/bin/MCPB.py", line 556, in <module>
> >>> premol2fs, cutoff, watermodel, 0, largeopt, sqmopt, smchg, lgchg)
> >>> File
> >>> "/home/Software/amber16/lib/python2.7/site-packages/mcpb/
> >> gene_model_files.py",
> >>> line 1745, in gene_model_files
> >>> ionids, chargedict, lgchg, outf, watermodel, largeopt, sqmopt)
> >>> File
> >>> "/home/Software/amber16/lib/python2.7/site-packages/mcpb/
> >> gene_model_files.py",
> >>> line 1441, in build_large_model
> >>> chargedict, IonLJParaDict, largeopt)
> >>> File
> >>> "/home/Software/amber16/lib/python2.7/site-packages/msmtmol/gauio.py",
> >> line
> >>> 156, in write_gau_mkf
> >>> chg = int(round(chargedict[ionname], 0))
> >>> KeyError: 'FE'
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> Thanking You;
> >>> With Regards;
> >>> Aashish Bhatt (PhD scholar ,India)
> >>> _______________________________________________
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> >>
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Received on Wed Jan 31 2018 - 08:00:03 PST
