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>? That could be the reason.
Kind regards,
Pengfei
> On Jan 8, 2018, at 10:47 PM, Aashish Bhatt <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>)* 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 -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
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> 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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Received on Tue Jan 16 2018 - 12:30:02 PST
