Hi Li Zhen,
Thanks for the recommendation. I was about to combine all chains into 1 but I’ll take the recommendation into consideration. I’m actually focusing on the ni cofactor in the active sites and its interactions with the ligands. Really appreciate the assistance and advice.
Thanks heaps,
Ingso
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________________________________
From: Li, Zhen <lizhen6.chemistry.msu.edu>
Sent: Monday, July 8, 2024 1:45:56 PM
To: Ingso Limbu <i.limbu.student.uq.edu.au>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: MCPB.py questions
Hi Ingso,
(Sorry one typo while answering Q1: I meant GLU, not GLY)
Coenzyme M reductase is a large complex with 6 chains, judged by PDB. If at least three chains need MCPB.py, I would recommend building three folders, one for each chain of the protein. Then, run MCPB.py for each folder to generate related frcmod (step 2), mol2 (step 3) and pdb + tleap.in (step 4) files.
Finally, copy all the frcmod and mol2 files to the fourth folder and combine the three tleap.in files into one (also combine three pdb files into one). As stated above, you may find the tleap and pdb files in step 4 of MCPB.py.
To be cautious, trying with a simple system first is always better than trying the whole system. If the research is to look into Zn2+ interacting with chains A and D in 1HBN, there is no need to involve too many other chains. Just some personal suggestions.
_____________________
Zhen Li<
http://lizhen62017.wixsite.com/home>, Ph.D.,
He/Him/His,
The Merz Research Group<
http://merzgroup.org>,
Rm. 287, Department of Chemistry,
578 S Shaw Ln., Michigan State University,
48824, MI.
________________________________
From: Ingso Limbu <i.limbu.student.uq.edu.au>
Sent: Sunday, July 7, 2024 11:22 PM
To: Li, Zhen <lizhen6.chemistry.msu.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: MCPB.py questions
Hi Li Zhen,
Thanks for the reply. Regarding the 2nd question, my protein is 1HBN and in the metal bonded model, there are atleast 3 chains involved. I want to get topology for the protein to run MD in gromacs.
Any advice and MCPB.py states only 1 chain in their documentation. Appreciate any help thanks.
Kind regards,
Ingso
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________________________________
From: Li, Zhen <lizhen6.chemistry.msu.edu>
Sent: Monday, July 8, 2024 1:13:38 PM
To: AMBER Mailing List <amber.ambermd.org>; Ingso Limbu <i.limbu.student.uq.edu.au>
Subject: Re: MCPB.py questions
Hi Ingso,
For question 1, yes, pdb4amber has the --reduce keyword that supports adding hydrogens, but that may not treat GLY and HIS properly like H++ does. Maybe experts in pdb4amber can give more suggestions.
For question 2, manually combining two chains into one will disturb the total charge of each system. For example, if both chain A and chain B are supposed to be neutral, combining them will make chain A +0.5 and chain B -0.5 charge instead. Running MCPB.py twice, once for each
So far, these two questions have nothing really related to MCPB.py's core code. So, the email title might be a bit confusing.
The ultimate purpose of MCPB.py is to provide frcmod files to build a bonded model for the metal center and its related small/large ligand systems.
MCPB.py should support modified residues because the charge fitting steps are done by QM, not MM.
If any MCPB.py-related problem persists, please feel free to send the error message.
Best regards,
Zhen.
________________________________
From: Ingso Limbu via AMBER <amber.ambermd.org>
Sent: Thursday, July 4, 2024 12:23 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] MCPB.py questions
Hi Amber community,
Back with several questions on MCPB.py.
1.
I have a question on the command
ambpdb -p 0.15_80_10_pH6.5_4zf6.top<
https://urldefense.com/v3/__https://ambermd.org/tutorials/advanced/tutorial20/files/mcpbpy_heme/0.15_80_10_pH6.5_4zf6.top__;!!HXCxUKc!1DesmAJ8Js4BIjCwvzG6SktQHB4rkLHyEukE7nqzAJRzohW2ExyYC4fj_P4J4yZZZJoh439rAwt_8a4IBUemF9s$ > -c 0.15_80_10_pH6.5_4zf6.crd<
https://urldefense.com/v3/__https://ambermd.org/tutorials/advanced/tutorial20/files/mcpbpy_heme/0.15_80_10_pH6.5_4zf6.crd__;!!HXCxUKc!1DesmAJ8Js4BIjCwvzG6SktQHB4rkLHyEukE7nqzAJRzohW2ExyYC4fj_P4J4yZZZJoh439rAwt_8a4Ioq3_8y8$ > > Protein_H.pdb
It is stated that we do not use the H++ pdb file. Out of curiousity, if we were to use pdb4amber on the H++ pdb file, wouldnt it follow amber naming convention/scheme so it would not be that terrible of a step (?). Is there an advantage in using ambpdb in this case? I ask this because for my system, i am unable to use H++ due to modified amino acids and am using the tutorial: Simulating the Green Fluorescent Protein and Building a Modified Amino Acid Residue to help me parameterise my modified Aas. I am merging this tutorial with the MCPB.py and since i cant use H++ server, i wonder if applying pdb4amber on a modified pdb file is equally as "correct" as ambpdb on top/crd files of leap to generate a pdb file
1.
In the documentation, it states that MCPB.py only deals with 1 chain, if i rename multiple chains to 1 identifier, is this necessarily the correct way to treat the system? With the ter statements still intact?
Kind regards,
Ingso
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Received on Sun Jul 07 2024 - 21:00:02 PDT
