Hi Cooper,
Based on my experience, it seems like there is no atom has atom name as “H2” in the mol2 file. You can double check your mol2 file. Please let me know the result.
Kind regards,
Pengfei
> On Feb 21, 2016, at 9:58 PM, Taylor, Cooper <cooper.taylor1.richmond.edu> wrote:
>
> Hi,
>
> I'm trying to use MCPB.py on a complex with a ZN 4-coordinate metal center
> (two Cys, one Hid, and one water), but am receiving the error as shown
> below when the "MCPB.py -i xyz.in -s 1a" command is entered. I am using
> Amber 14 with AmberTools 15 on a Linux workstation running RedHat 6.7 using
> Python 2.7. We are not including a ligand in this process.
>
> The xyz.in file looks like:
>
> original_pdb xyz_fixed_H.pdb
>
> group_name xyz
>
> cut_off 2.8
>
> ion_ids 3111
>
> ion_mol2files ZN.mol2
>
> naa_mol2files ZN.mol2 WAT.mol2
>
> The error message is as follows:
>
> Traceback (most recent call last):
>
> File "/usr/local/amber/amber14/bin/MCPB.py", line 419, in <module>
>
> watermodel, 2, sqmopt)
>
> File
> "/usr/local/amber/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> line 1167, in gene_model_files
>
> ionids, chargedict, totchg, outf, watermodel, sqmopt)
>
> File
> "/usr/local/amber/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> line 984, in build_large_model
>
> chg = str(int(chargedict[i]))
>
> KeyError: 'H2'
>
> I followed the tutorial, and have separated out the metal center as well as
> the water, creating separate PDB files and mol2 files for each. Any
> assistance would be appreciated.
>
> Thanks,
> Cooper
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Received on Mon Feb 22 2016 - 07:30:03 PST
