Re: output results to phenix

From: Ropon-Palacios G. (
Date: Mon Feb 01 2021 - 12:04:27 CST

You can use PDBalias sytaxis for this.


From: <> on behalf of Ming Sun <>
Reply-To: <>, Ming Sun <>
Date: Monday, February 1, 2021 at 12:29 PM
To: "" <>
Subject: namd-l: output results to phenix


Dear All


I'm trying to output the MDFF results to Phenix, for finer tuning. However, I kept having format issues. Any insight would be appreciated. Thank you!


Here are what I did,


output single frame from dcd

convert HSE/HSD to HIS

convert CD ILE to CD1 ILE

convert O1P to OP1, O2P to OP2

(it has nucleic acids) convert THY to DT ...

write out PDB without "H"


(did I miss any pdb alias? thanks!)






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