[AMBER] Error in Gausian file preparation using MCPB.py

From: gagandeep singh <gagan.sk.1994.gmail.com>
Date: Sat, 25 Jul 2020 03:25:47 +0530

Hi All,
I was running MCPB.py fto prepare gaussian file for my system having Fe2+
ion surrounded by ASp and AKG. It gave the following error:

**=======================Building models==========================**

the small model...It contains the residue 126-ASP as sidechain
coordinated.It contains the residue 206-FE as normal.It contains the
residue 207-AKG as normal.Totally there are 27 atoms in the small
model.Totally there are 137 electrons in the small model.***Creating the
standard model...It contains the residue 126-ASP as normal.Traceback (most
recent call last): File "/home/gsk/miniconda3/bin/MCPB.py", line 644, in
<module> addred, lgchg, lgspin) File
line 1908, in gene_model_files bdedatms, addbpairs, libdict, autoattyp)
line 1472, in build_standard_model attype = libdict[resname + '-' +
atname][0]KeyError: 'ASP-HB1'*

Looks like there is a problem with my pdb file and naming of residues is
not compatible with amber. I saved the pdb in chimera with the output
option for serial numbering as amber,still got this error.
Any suggestions on how to prepare my protein in order to overcome this
Gagandeep Singh
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Received on Fri Jul 24 2020 - 15:00:05 PDT
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