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 - 21:00:02 PDT
