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/
> 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
> >
>
>
>
> --
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 29 2017 - 22:00:04 PDT
