Re: [AMBER] HMR with ParmEd for PSF/PDB inputs?

From: Jason Swails <>
Date: Sat, 10 Dec 2016 22:46:57 -0500

On Fri, Dec 9, 2016 at 12:28 PM, Brian Radak <>

> ParmEd can't infer atomic numbers based on mass or atom names?

‚ÄčIt does sometimes, but PSF files I believe I largely expected people to
load RTF and PRM files into them (which *will* contain the atomic number
and avoid the need to infer them).

ParmEd has inference code, but I'm not sure that it's ever applied to PSF
files... Also, the<action>.execute() are not always
guaranteed to work on non-Amber topologies, but I believe HMR is one that

All the best,

Jason M. Swails
AMBER mailing list
Received on Sat Dec 10 2016 - 20:00:02 PST
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