Hi Anna,
Please use the newest version of MCPB.py: https://github.com/Amber-MD/pymsmt/releases/tag/v2.0c <https://github.com/Amber-MD/pymsmt/releases/tag/v2.0c>. It could handle more different situations. I tried your case on my own laptop and it works fine. Please let me know if you still has a problem.
Kind regards,
Pengfei
> On Jul 20, 2016, at 8:44 AM, Anna Cebrian Prats <Anna.Cebrian.uab.cat> wrote:
>
> Hi,
>
> I'm using MCPB.py for building parameters of the coordinate sphere of an iron inside a protein and I'm following the same steps as described in MCPB tutorial.
>
> When I execute this: MCPB.py -i LOX15.in -s 1
>
> I get this error message:
>
> ******************************************************************
> * *
> *=======================Building models==========================*
> * *
> ******************************************************************
> ***Creating the sidechain model...
> It contains the residue 360-HID
> It contains the residue 365-HID
> It contains the residue 540-HID
> It contains the residue 544-HIE
> It contains the residue 662-ILE
> It contains the residue 663-FE
> It contains the residue 664-OH
> Totally there are 81 atoms in the sidechain model.
> Totally there are 291 electrons in the sidechain model.
> ***Creating the standard model...
> It contains the residue 360-HID
> It contains the residue 365-HID
> It contains the residue 540-HID
> It contains the residue 544-HIE
> It contains the residue 662-ILE
> Traceback (most recent call last):
> File "/opt/AMBER/amber14/bin/MCPB.py", line 410, in <module>
> watermodel, 2, sqmopt)
> File "/opt/AMBER/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py", line 1164, in gene_model_files
> libdict, autoattyp)
> File "/opt/AMBER/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py", line 355, in build_standard_model
> attype = libdict[resname + '-' + atname][0]
> KeyError: 'ILE-OXT'
>
> -----------------------
>
> I guess that the program doesn't understand that CILE (C-terminal Isoleucine) is bonded to the Fe by the oxygen atom that close the c-terminal, called OXT by Amber.
>
>
> O
> /
> -C
> \
> OXT --- Fe
>
>
> I was wondering if could be possible to treat the CILE as a ligand, but I believe that then the CILE won't be bonded to the protein...
>
> In this email I added the files that I am using
>
> I will appreciate some help. Thank you.
>
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Received on Wed Jul 20 2016 - 07:30:02 PDT
