Hi,
the leap output tells you that your input pdb file seems to contain
errors in atom naming: there is no atom with name 'H' in N-terminal
residues, so correct your input file.
Furthermore, I noticed that KCX.mol2 and KCX_by_parmchk2.mol2 have
different conformations (no problem) and protonations, i.e. structures
(potential problem).
Since you are dealing with an advanced simulation setup - I did not read
through your setup protocol and retries in detail -, the above hints may
just be the begin of further trouble shooting ...
Good luck,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 21.10.2024 um 09:04 schrieb 郑逸非 via AMBER:
> 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 - 04:30:01 PDT
