Hi Cooper,
Can you send me these files: xyz.in, xyz_fixed_H.pdb, ZN.mol2, and WAT.mol2 in an independent email (to my email address: ambermailpengfei.gmail.com)? I can help to check them.
Kind regards,
Pengfei
> On Feb 22, 2016, at 10:17 AM, Taylor, Cooper <cooper.taylor1.richmond.edu> wrote:
>
> 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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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
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Received on Mon Feb 22 2016 - 07:30:05 PST
