Hi Ingso,
I am not sure why NIA and NID need to be distinguished from the residue level… They could be both called NI, since the 1HBN.in file already specified the atom ID to be 38021.
Also, regarding our previous discussions, please feel free to remove TER between chains for a multiple-chain MCPB.py. Pengfei confirmed that it is doable.
Best regards,
Zhen
>
> On Jul 21, 2024, at 4:22 PM, Ingso Limbu via AMBER <amber.ambermd.org> wrote:
>
> Hi Amber community,
> Running step 1 of MCPB and i get a keyerror.
> Now, i have seen the warnings about this error and what it could potentially be and i have tried to explore those options but it doesnt seem to work.
>
> My pdb file:
> HETATM38021 NI NIA 2480 30.430 30.940 -6.768 1.00 10.27 NI
> HETATM38022 NI NID 2481 34.389 36.409 -58.183 1.00 10.66 NI
>
> In my 1HBN.in file:
> ion_ids 38021
> ion_mol2files NIA.mol2
>
> Mol2 file:
> .<TRIPOS>MOLECULE
> NIA
> 1 0 1 0 0
> SMALL
> User Assigned Charge
>
>
> .<TRIPOS>ATOM
> 1 NI 30.4300 30.9400 -6.7680 NI 1 NIA 1.000000
> .<TRIPOS>BOND
> .<TRIPOS>SUBSTRUCTURE
> 1 NIA 1 TEMP 0 **** **** 0 ROOT
>
> I think i am placing the right definitions for NIA (residue) and NI (atom) but i still get the error
> chg = int(round(chargedict[ionname], 0))
> ~~~~~~~~~~^^^^^^^^^
> KeyError: 'NI'
>
> I have two (duplicate) active sites therefore A and D. I want to get the frcmod for one active site and just apply across to both active site. This protein is 1HBN. Any advice on what i can do?
>
> TIA
>
>
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Received on Mon Jul 22 2024 - 15:00:02 PDT
