Hi Ingso,
Apology for my late reply again. It took a while to digest. To make my answer simpler, please see answer to Q1.1 of this page
https://ambermd.org/tutorials/advanced/tutorial20/mcpbpyfaq.php
In short, you may modify $AMBERHOME/AmberTools/src/pymsmt/pymsmt/mol/element.py so it will include NIA and NID. I just checked that the file only has four instances of NI.
Duplicate NI information behind thoses instances of NI, and only change names to NIA/NID, it should work as a way around.
If you do not have access to AMBER source code. I would recommend contacting your local HPC cluster support. Hope it helps.
Best regards,
Zhen
From: Ingso Limbu <i.limbu.student.uq.edu.au>
Date: Monday, July 22, 2024 at 6:00 PM
To: Li, Zhen <lizhen6.chemistry.msu.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] MCPB.py keyerror
Hi Li Zhen,
Thanks for the reply. Regarding the split, when we want to define mol2 files, they 1) have coordinates of individual residues 2) charges as well. Also, I thought the name of the residue must match the mol2 file names so I split it into two different entities(residues). So that in tleap I can load the mol2 of the individual residues. They are essentially the same parameters since it is a symmetrical di-trimer. For now, I have changed NIA to NI since I believe the MCPB.py script only recognises the residue type without additional labels and it have worked so I am parameterising one active site and will carry/copy(appropriately) over the parameters to the other active site.
However, though it doesn't apply to my project, I wonder how someone will handle duplicate metal Centers in 1 big protein that are different active sites? Instead of splitting NI into NIA and NID, is there a way around it?
Kind regards,
Ingso
________________________________
From: Li, Zhen <lizhen6.chemistry.msu.edu>
Sent: Tuesday, July 23, 2024 7:47:15 AM
To: Ingso Limbu <i.limbu.student.uq.edu.au>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] MCPB.py keyerror
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 Aug 05 2024 - 09:00:02 PDT
