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 Mon Jan 08 2018 - 21:00:02 PST
