AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber prep question

From: case (case_at_biomaps.rutgers.edu)
Date: Thu Jul 09 2009 - 11:48:44 CDT

On Thu, Jul 09, 2009, Andrew Olson wrote:

> Here it is, taken straight from the dlg file, my starting point before adding Hs and charges.  

You have to add the hydrogens (not the charges) *before* sending the file to
antechamber. (sleap can automatically add hydrogens, but it is usually safer
to do it manually, especially for a charged ion.) Your file has hydrogens on
polar atoms, but is missing the hydrogens on the carbon atoms.

...dac

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