Hi Sushi,
I guess there is something wrong with your original PDB file or your input file. Can you send them to me? If you prefer, you can send them to my email directly.
Kind regards,
Pengfei
> On May 30, 2017, at 11:15 PM, Sushi Shilpa <sushishilpa.gmail.com> wrote:
>
> Dear sir,
>
> Thank you so much for your kind help. I have changed residue name as ARS
> and its atom name as AS, I have given the cutoff in xyz.in 2.9, but the
> residue MET is in the position 9.8 Angstrom away from As ion, but it is
> still considering MET, and I am getting again an error given below.
>
> It contains the residue 11-MET as sidechain coordinated.
> It contains the residue 12-CYS as sidechain coordinated.
> It contains the residue 13-CYS as sidechain coordinated.
> It contains the residue 18-CYS as sidechain coordinated.
> Totally there are 43 atoms in the small model.
> Totally there are 185 electrons in the small model.
> ***Creating the standard model...
> It contains the residue 11-MET as normal.
> Traceback (most recent call last):
> File "/home/camp/Desktop/Amber14/amber14/bin/MCPB.py", line 569, in
> <module>
> premol2fs, cutoff, watermodel, 2, largeopt, sqmopt, smchg, lgchg)
> File "/home/camp/Desktop/Amber14/amber14/bin/mcpb/gene_model_files.py",
> line 1742, in gene_model_files
> bdedatms, libdict, autoattyp)
> File "/home/camp/Desktop/Amber14/amber14/bin/mcpb/gene_model_files.py",
> line 1319, in build_standard_model
> attype = libdict[resname + '-' + atname][0]
> KeyError: 'MET-AS'
>
>
> I have attached xyz_small.pdb, please take a look at this, metal ion has
> atom name AS but residue name changed to MET.
>
> Regards,
>
> Shilpa T
>
> On Tue, May 30, 2017 at 10:39 PM, Pengfei Li <ambermailpengfei.gmail.com>
> wrote:
>
>> Hi Sushi,
>>
>> As3+ is a special case, you need to have its Residue name as “ARS”, and
>> its atom name as “AS” in the corresponding pdb and mol2 files.
>>
>> Please let me know whether it solves the problem.
>>
>> Kind regards,
>> Pengfei
>>
>>> On May 29, 2017, at 7:35 AM, Sushi Shilpa <sushishilpa.gmail.com> wrote:
>>>
>>> Hi,
>>>
>>>
>>>
>>> I'm trying to use MCPB.py on a complex with a As and three CYS, but I am
>>> receiving the error as shown below when the "MCPB.py -i xyz.in -s 1"
>>> command is entered. I am using Amber 14 with AmberTools 15 on a Linux
>> and
>>> Python 2.7.
>>>
>>>
>>>
>>>
>>>
>>> The xyz.in file looks like:
>>>
>>>
>>>
>>> original_pdb xyz_fixed_H.pdb
>>>
>>> group_name xyz
>>>
>>> cut_off 4
>>>
>>> ion_ids 1
>>>
>>> ion_mol2files AS.mol2
>>>
>>> naa_mol2files AS.mol2 WAT.mol2
>>>
>>>
>>>
>>>
>>>
>>> The error message is as follows:
>>>
>>>
>>>
>>>
>>> Totally there are 25 atoms in the sidechain model.
>>> Traceback (most recent call last):
>>> File "/home/camp/Desktop/Amber14/amber14/bin/MCPB.py", line 555, in
>>> <module>
>>> cutoff, watermodel, 2, largeopt, sqmopt, scchg, lgchg)
>>> File
>>> "/home/camp/Desktop/Amber14/amber14/lib/python2.7/site-
>> packages/mcpb/gene_model_files.py",
>>> line 1713, in gene_model_files
>>> scresant, scresact, scresknh, screskco, scchg, outf, sqmopt)
>>> File
>>> "/home/camp/Desktop/Amber14/amber14/lib/python2.7/site-
>> packages/mcpb/gene_model_files.py",
>>> line 1214, in build_sidechain_model
>>> AtNum = Atnum[gatm.element]
>>> KeyError: 'A'
>>>
>>>
>>>
>>> Please help me to fix this issue.
>>>
>>>
>>>
>>> Regards,
>>>
>>> Shilpa T
>>> _______________________________________________
>>> 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
>>
> <ArsD_small.pdb>_______________________________________________
> 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 Wed May 31 2017 - 15:00:02 PDT
