this command is not working Andrew i am using amber 16 is go3 not buitin
i have all the input files for this command
g03 < 4ZF6_small_opt.com
<
http://ambermd.org/tutorials/advanced/tutorial20/files/mcpbpy_heme/4ZF6_small_opt.com>
> 4ZF6_small_opt.log
On Thu, Jun 29, 2017 at 11:30 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> oh yes it run now. Andrew i use
>
> 2.000000 charge for FE ferrous oxidation state
>
> and use 2.8 cutoff by default from the 4ZF6 <http://ambermd.org/tutorials/advanced/tutorial20/files/mcpbpy_heme/4ZF6.in>.in file. is it write ??
>
>
> On Thu, Jun 29, 2017 at 11:18 PM, Andrew Schaub <aschaub.uci.edu> wrote:
>
>> Based off of your output, and lack of an .input file, I am assuming the
>> following. You most likely copied the input script from the tutorial, but
>> forgot to change the ions_id.
>>
>> original_pdb 4ZF6_H_renum.pdb
>> group_name 4ZF6
>> cut_off 2.8
>> *ion_ids 7440*
>> software_version g09
>> ion_mol2files FE.mol2
>> naa_mol2files HEM.mol2 1PE.mol2 EDO.mol2
>> frcmod_files HEM.frcmod 1PE.frcmod EDO.frcmod
>>
>> If you open up your HNOXO_H_renum.pdb, scroll down to where the Fe is, and
>> find the atom number. Change your ions_id to match the atom number there.
>> In the original tutorial, the Fe atom ID was pulled from 4ZF6_H_renum.pdb,
>> by finding this line in the PDB file:
>>
>> HETATM *7440 FE* FE A 462 -7.890 0.888 28.105 1.00
>> 38.80 FE
>>
>> Best Regards,
>>
>> Drew
>>
>>
>>
>>
>> On Thu, Jun 29, 2017 at 7:44 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
>> wrote:
>> >
>> > The following is the input variable you have:
>> > The variable ion_ids is : [7440]
>> > The variable ion_info is : []
>> > The variable ion_mol2files is : ['FE.mol2']
>> > The variable original_pdb is : HNOXO_H_renum.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 : HNOXO
>> > 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
>> > Traceback (most recent call last):
>> > File "/home/rehan/Downloads/amber16/bin/MCPB.py", line 498, in
>> <module>
>> > addbpairs)
>> > File
>> >
>> "/home/rehan/Downloads/amber16/lib/python2.7/site-packages/
>> mcpb/gene_model_files.py",
>> > line 50, in get_ms_resnames
>> > resid = mol.atoms[i].resid
>> > KeyError: 7440
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>>
>> --
>> Andrew Schaub
>> Graduate Program in Chemical & Structural Biology
>> Tsai Lab, http:///www.tsailabuci.com/
>> Luo Lab, http://rayl0.bio.uci.edu/html/
>> University of California, Irvine
>> Irvine, CA 92697-2280
>> 949-824-8829 (lab)
>> 949-877-9380 (cell)
>> aschaub.uci.edu
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Thu Jun 29 2017 - 21:30:02 PDT
