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 - 20:30:02 PDT
