Hi Vinicius,
Did you try pdb4amber? Did that fail?
What do the names correspond to; is it the variant of the OPLS forcefield that Schrödinger uses?
Best,
Matthew
> On Sep 15, 2023, at 5:30 PM, Vinicius Cruzeiro (Vinny) via AMBER <amber.ambermd.org> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> 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
