Hi Cooper,
I got your files and suggested you to
1) Change the line of naa_mol2files to “naa_mol2files WAT.mol2”
2) Renamed the mol2 file of water to exactly: “WAT.mol2” (based on the files you sent to me it seems you were not using this file name).
This is because ZN.mol2 is already in ion_mol2files line, so you don’t need to specify it in the naa_mol2files line again.
The other thing is that the mol2 file name should be the exactly same as the corresponding residue name in the PDB file.
Please let me know whether it helps.
Kind regards,
Pengfei
> On Feb 22, 2016, at 10:26 AM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
>
> 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
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 22 2016 - 08:00:05 PST
