Hi Abhishek,
This problem is because an error in your PDB file, which has a HIE residue that has a HD1 atom in it (MCPB.py could not find parameters for this HD1 atom so it gave an error). This is not correct since HIE should not have this atom due to HIE has protonation on the epsilon nitrogen (not the delta nitrogen).
Pengfei
> On Jan 24, 2018, at 2:43 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
>
> Hi everyone,
>
> I have a system with zinc surrounded by Hie. So while generating gaussian input file I am getting following error
>
>
> ***Creating the small model...
> It contains the residue 530-HIE as sidechain coordinated.
> It contains the residue 534-HIE as sidechain coordinated.
> It contains the residue 593-GLU as sidechain coordinated.
> It contains the residue 696-ZN as normal.
> It contains the residue 697-MOL as normal.
> It contains the residue 698-HOH as normal.
> Totally there are 83 atoms in the small model.
> Totally there are 328 electrons in the small model.
> ***Creating the standard model...
> It contains the residue 530-HIE as normal.
> Traceback (most recent call last):
> File "/nethome/axt651/apps/amber16_tools/bin/MCPB.py", line 644, in <module>
> addred, lgchg, lgspin)
> File "/nethome/axt651/apps/amber16_tools/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py", line 1898, in gene_model_files
> bdedatms, libdict, autoattyp)
> File "/nethome/axt651/apps/amber16_tools/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py", line 1471, in build_standard_model
> attype = libdict[resname + '-' + atname][0]
> KeyError: 'HIE-HD1'
>
> Kindly help me how to solve this problem.
>
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Received on Thu Jan 25 2018 - 11:00:04 PST
