Hi Yifei,
May I know the reason for your change from 4CEU to 6RKG? I am still working on the MCPB.py tutorial for the modified residues based on 4CEU, but that got delayed for multiple reasons. Will give more updates by the end of this month. Thank you for waiting, and hopefully, it will work for 6RKG as well since that is also a urease.
Best regards,
Zhen.
From: 郑逸非 via AMBER <amber.ambermd.org>
Date: Monday, October 21, 2024 at 3:06 AM
To: amber <amber.ambermd.org>
Subject: [AMBER] Assistance Required with MCPB.py and Non-Standard Residue Handling
Dear Amber managers and users,
I am currently working with MCPB.py to model the interaction of nickel ions with the active site of urease. During this process, I encountered an issue with a non-standard residue in the protein's main chain. I had previously sought advice and was advised to customize the KCX residue and then provide the frcmod and mol2 parameters to both MCPB.py and tleap's input files.
I have successfully processed the KCX residue and generated the frcmod and mol2 files. However, upon comparing the atom numbers and types in the .frcmod file with those in the .pdb file, I noticed discrepancies in the order and naming of atoms, as well as an additional hydrogen atom in my .frcmod file. This leads me to believe that I should regenerate the .frcmod file.In my attempt to regenerate the .frcmod file, I followed the MCPB.py tutorial to generate all necessary files. However, when I used the command "parmchk2 -i KCX.mol2 -o KCX.frcmod -f mol2" to generate the .frcmod file, the content seemed incomplete compared to my previous generation. I proceeded without much attention to this issue. Then it led to my first question: "H++ seems unable to handle a structure that is not complete, specifically with the KCX residue as its backbone." To address this, I used pdbfixer to add hydrogen atoms, although I am uncertain if this was the correct approach.
Subsequently, I followed the tutorial, and everything appeared to progress smoothly until I reached the step "Using tleap to generate the topology and coordinate files" with the command tleap -s -f 6rkg_tleap.in > 6rkg_tleap.out. At this point, I encountered a second issue: "tleap displayed a Fatal Error."
I have attached the relevant files for your review and hope that you can provide insights into my questions. Thank you very much for your assistance! If there are any additional files required, please let me know, and I will be happy to provide them.
Best regards.
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Received on Mon Oct 21 2024 - 21:30:01 PDT
