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
> _______________________________________________
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> 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
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Received on Thu Jun 29 2017 - 20:30:04 PDT
