Re: [AMBER] Maestro PDB to Amber PDB

From: He, Amy via AMBER <amber.ambermd.org>
Date: Fri, 15 Sep 2023 22:19:17 +0000

Hi,

We have also been using pdb4amber to rename residues (mainly the cysteine residues that form disulfide bonds, and the 2 neutral tautomers of histidine residues). Please search pdb4amber in the Amber manual, or take a look at: https://ambermd.org/tutorials/basic/tutorial9/index.php

Additionally, the naming of some hydrogens in residues at termini may not be recognized by some protein force fields in Amber. We have encountered similar problem with the capping units NME and ACE. If you’re ok with some minor changes in the positions of these hydrogens, you could remove the mismatched hydrogens and let Leap rebuild the hydrogens based on the force field you choose.

Bests, 


--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Lab
Ohio State University
he.1768.osu.edu<mailto:he.1768.osu.edu>
From: Vinicius Cruzeiro (Vinny) via AMBER <amber.ambermd.org>
Date: Friday, September 15, 2023 at 5:31 PM
To: Jing Qu via AMBER <amber.ambermd.org>
Subject: [AMBER] Maestro PDB to Amber PDB
Hello all,
I am working with a PDB file that was generated by Schrodinger’s Maestro software. However, I need to convert it to an Amber PDB file format for further analysis. The main challenge is that the atom naming conventions are different between the two formats, especially for the hydrogen atoms. Also, some residue names may change due to different protonation states.
I am looking for a reliable and efficient way to perform this conversion. I am wondering if anyone here has already a good solution for this. If there is an existing script or tool that can do this task, please let me know where I can find it.
Thank you,
Vinícius Wilian D. Cruzeiro, PhD
Scientist II, Computational Chemistry
Architect Therapeutics
Twitter: .vwcruzeiro
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Received on Fri Sep 15 2023 - 15:30:02 PDT
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