Andrew one more thing i want to ask , i prepare the file for heme
containing protein but in our case the heme fe-----NO in one system and
other it bonded with O2 how i can add it because i need to study when NO
attach AND when O2 attach what changes occur so in that case how i add NO
and O2 in the system
On Fri, Jun 30, 2017 at 12:38 AM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> That's great
>
> On Jun 30, 2017 12:30 AM, "Andrew Schaub" <aschaub.uci.edu> wrote:
>
>> As Elvis stated. You need Gaussian. But good news, The University of
>> Michigan has access to it. http://arc-ts.umich.edu/software/gaussian/
>>
>> Best Regards,
>>
>> Drew
>>
>>
>> On Thu, Jun 29, 2017 at 9:15 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
>> wrote:
>>
>> > 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/mcpbp
>> y_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
>> > >> > _______________________________________________
>> > >> > AMBER mailing list
>> > >> > 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
>> > >>
>> > >
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Andrew Schaub
>> Graduate Program in Chemical & Structural Biology
>> Tsai Lab, http:///www.tsailabuci.com/ <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 <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Thu Jun 29 2017 - 22:30:02 PDT
