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/#>
>
>
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> in/elvisadrianmartis/>
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>
>
>
> ________________________________
> 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
> >>
> >
> >
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Received on Thu Jun 29 2017 - 21:30:04 PDT
