If you have an account on the HPC to run Amber, then your account probably
already has access to Gaussian. The people at ARC-TS should be able to help
you with the Gaussian portion of this, then you'll take the output from
Gaussian and feed it back into MCPB. Your almost there.
Good Luck!
Drew
On Thu, Jun 29, 2017 at 9:26 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> So in that case is there any other way use mcpb.py input files like go3
>
> On Jun 30, 2017 12:19 AM, "Elvis Martis" <elvis.martis.bcp.edu.in> wrote:
>
> > Hi Rana,
> >
> > "g03" is a Gaussian 03 command and Gaussian 03 or 09 or 2016 is not a
> part
> > of AMBER or AMBERTOOLS and has to be purchased separately.
> >
> >
> > Best Regards
> >
> > [photo]
> >
> >
> >
> > Elvis Martis
> > Ph.D. Student (Computational Chemistry)
> > at Bombay College of Pharmacy
> >
> >
> > A Kalina, Santacruz [E], Mumbai 400098, INDIA
> > W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
> > Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
> >
> >
> > [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
> > ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
> > yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
> > d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
> > icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
> > in/elvisadrianmartis/>
> >
> >
> >
> >
> >
> > ________________________________
> > From: Rana Rehan Khalid <rrkhalid.umich.edu>
> > Sent: 30 June 2017 09:45:47
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default
> > ions 7440
> >
> > 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
> > >> > _______________________________________________
> > >> > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
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/>
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Received on Thu Jun 29 2017 - 22:00:03 PDT
