[AMBER] Protonation Question

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From: ElBagoury, Abdulrahman Walid Attia Ibrahim via AMBER <amber.ambermd.org>
Date: Mon, 4 May 2026 17:54:37 +0000

Hello amber members,

I have a question , if I have protonated using MOE and want to use the ambertools to solvate my protein , if i used pdb4amber and then used --nodry to remove the hydrogens , after getting to to tleap ,will it re-add the the hydrogens in the same manner as did in MOE but written in amber naming convention ?

Best Regards,
Abdulrahman
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Received on Mon May 04 2026 - 11:00:02 PDT