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

From: Brian Radak <brian.radak.accts.gmail.com>
Date: Sun, 11 Dec 2016 12:21:23 -0600

So what is the correct syntax for loading RTF and PRM files into a PSF
object?


On 12/10/2016 09:46 PM, Jason Swails wrote:
> On Fri, Dec 9, 2016 at 12:28 PM, Brian Radak <brian.radak.accts.gmail.com>
> wrote:
>
>> 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 parmed.tools.<action>.execute() are not always
> guaranteed to work on non-Amber topologies, but I believe HMR is one that
> does.
>
> All the best,
> Jason
>

-- 
Brian Radak
Postdoctoral Scholar
Gordon Center for Integrative Science, W323A
Department of Biochemistry & Molecular Biology
University of Chicago
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
email: radak.uchicago.edu
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Received on Sun Dec 11 2016 - 10:30:02 PST
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