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
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Received on Tue May 30 2017 - 10:30:02 PDT
