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...
I will appreciate some help. Thank you.
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Received on Wed Jul 20 2016 - 07:00:03 PDT
