Re: [AMBER] viewing PREPIN/PREPC files

From: David A Case <>
Date: Mon, 1 Jul 2013 21:21:42 -0400

On Mon, Jul 01, 2013, Rejwan wrote:
> Besides XLEAP, is there alternative way to view Prepin/Prepc molecules
> and atoms and definations  preferably in Windows 

1. Use a text editor (your favorite).

2. Use LEaP to convert prep files to mol2 format; then either use a text
editor or lots of visualization programs (Vmd, Chimera, PyMol, etc.) to
visualize the mol2 file. Chimera has the closest integration with amber
(look at the Amber menu in Chimera).

Option 2 is probably the best: we are trying to retire the prep format, since
it is not needed for anything, is nonstandard, and has some funny behaviors.
It is still around because people have workflows that expect it, which they
would prefer not to have to update. But in most circumstances, the mol2
format should be preferred.


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Received on Mon Jul 01 2013 - 18:30:02 PDT
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