On Wed, Mar 18, 2015 at 11:27 AM, Brian Radak <brian.radak.accts.gmail.com>
wrote:
> Oh that worked great! I had heard tell of the "chamber" command in parmed
> but could not find it in the documentation (bc I only have the Amber14
> release manual duh).
>
> Semi-related follow-up: If I want to compare energies between NAMD and
> AMBER, do I need any special flags in mdin? Is 1-4 scaling automagically
> switched to CHARMM values?
>
You're trying to compare Amber with chamber prmtop to NAMD with CHARMM
psf, correct? Because NAMD won't know what to do with a CHAMBER topology
file.
In that case, I would suggest starting from George's Amber-in-NAMD guide
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 18 2015 - 09:00:04 PDT
