Thank you so much everyone!
Vinícius Wilian D. Cruzeiro, PhD
Scientist II, Computational Chemistry
Architect Therapeutics
Twitter: .vwcruzeiro
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Sunday, September 17, 2023 8:08 AM
To: Vinicius Cruzeiro (Vinny) <vcruzeiro.architecttherapeutics.com>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Maestro PDB to Amber PDB
On Fri, Sep 15, 2023, Vinicius Cruzeiro (Vinny) via AMBER wrote:
>
>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.
Amber tries to follow the PDB standard closely, so you have a legitimate
complaint to Schrodinger if you file doesn't comply. Plus, they might be
aware of ways to "clean up" files that Maestro creates.
Running the PDB file through pdb4amber will clean up a lot of things. You
might need to run in twice, once to see if it can fix protonation states
(although I think that only helps for histidine); then a second time to
remove hydrogens: LEaP will build them back in with correct names.
...hope this helps...dac
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Received on Mon Sep 18 2023 - 16:00:02 PDT
