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> 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 -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>>
> 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>>? 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>>
>> 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>>)*
>> 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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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Thu Jan 25 2018 - 11:00:03 PST
