AMBER Archive (2008)

Subject: Re: AMBER: using packmol file in Amber

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Dec 05 2008 - 09:58:51 CST

On Fri, Dec 05, 2008, oguz gurbulak wrote:
>
> xleap -s -f leaprc.gaff
> octane = loadpdb octane.gaff.pdb
> saveoff octane octane.lib
> Quit

This won't work at all. The pdb file only has coordinates and atom/residue
names in it; it doesn't have any atom types or charges that were generated
by antechamber.

You need to load the prepi file that antechamber created if you want to create
a .lib file. You don't really need the lib file here. Load the prepi file,
the frcmod file, and then the pdb file. That way, leap has all the information
it should need.

....dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu