Hi Zhen,
Thanks for the prompt response.
More so than MCPB.py, it's the H++ server for the step on
We can use the webserver H++<
http://biophysics.cs.vt.edu/> (here we use the default settings) to add hydrogen atoms to the PDB file. H++ will delete the non-standard residues during the modeling process. Along with generating the PDB file with hydrogen atoms, it will also generate AMBER topology and coordinate files for the system. Then we can use the topology and coordinate files to generate PDB file, since this PDB file will use an AMBER naming scheme for the residues (e.g. HID, HIE, HIP but not HIS for Histidine). Here we perform the command:
ambpdb -p 0.15_80_10_pH6.5_4zf6.top<
https://ambermd.org/tutorials/advanced/tutorial20/files/mcpbpy_heme/0.15_80_10_pH6.5_4zf6.top> -c 0.15_80_10_pH6.5_4zf6.crd<
https://ambermd.org/tutorials/advanced/tutorial20/files/mcpbpy_heme/0.15_80_10_pH6.5_4zf6.crd> > Protein_H.pdb
Where the H++ server deletes my modified residues but the GFP tutorial you have loaded might do the trick and I can get the pdb file with the topology and coordinate file to replace the ambpdb step (atleast that's what I believe so.)
Thanks
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________________________________
From: Li, Zhen <lizhen6.chemistry.msu.edu>
Sent: Friday, June 21, 2024 9:53 PM
To: Ingso Limbu <i.limbu.student.uq.edu.au>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Modified amino acids in MCPB.py
Hi Ingso,
Do you have the specific error message from MCPB.py? As far as I know, the HEME tutorial should be compatible with modified residues. You may also need to consider the GFP tutorial (A26) of jointing the modified residue(s) to the main chain using an “mc” file while running “prepgen”.
Also, we are working on a FAQ page for MCPB.py. The text part is attached so please feel free to take a look.
Best regards,
Zhen.
From: Ingso Limbu via AMBER <amber.ambermd.org>
Date: Friday, June 21, 2024 at 6:18 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Modified amino acids in MCPB.py
Hi people,
I am following the MCPB.py tutorial and had several questions as I will be working on a rather complicated system.
PDB ID: 1HBN has 6 chains with several cofactors and modified amino acids.
1. My problem is when i tried to feed the pdb file to H++ server, due to modified amino acids i have issues, i can get a way around it by using PDB2PQR and parameterising it using antechamber but one tiny problem i have is that im not sure how MCPB.py is going to read/parameterise my modified amino acid residues.
2.
Also with multiple chains, if i rename the chains to one chain, is that enough to fix the problem?
3.
What is the protocol to getting around modified amino acids for MCPB.py
Apppreciate any help on the matter.
Kind regards,
Ingso
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Received on Fri Jun 21 2024 - 06:00:02 PDT
