Hi Pengfei,
Thank you for your response! I'm still at a loss because my mol2 file has
the atom name "H2". The file is copied below:
.<TRIPOS>MOLECULE
WAT
3 2 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 O -2.3030 -8.7460 14.2750 OW 193 WAT -0.785000
2 H1 -1.9620 -9.2290 14.2520 HW 193 WAT 0.392000
3 H2 -2.8520 -8.9550 14.3200 HW 193 WAT 0.392000
.<TRIPOS>BOND
1 1 2 1
2 1 3 1
.<TRIPOS>SUBSTRUCTURE
1 WAT 1 TEMP 0 **** **** 0 ROOT
Any thoughts on this?
Thanks,
Cooper
On Mon, Feb 22, 2016 at 10:10 AM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Feb 22 2016 - 07:30:04 PST
