Re: [AMBER] Reduce not working properly

From: David A Case <>
Date: Fri, 20 Mar 2015 08:44:45 -0400

On Thu, Mar 19, 2015, Francesco Gentile wrote:

> I am trying to use reduce to add hydrogens to one protein-ligand complex.
> However, it is not adding the hydrogens to the ligand (while it is working
> for the protein). Even if I try to run on the ligand alone I cannot get any
> added hydrogen (despite no errors are displayed); this is my ligand

Reduce doesn't add hydrogens to arbitrary molecules. It knows about standard
residues, and about what is in its "hetatm" dictionary, but nothing else.
You will need some other program to do this.

[For a "one-off" solution, I generally load the molecule into xleap, and use
it's commands to add hydrogens; (be sure to select each one and click on
"minimize selection" to get reasonably good geometries). But this works for
me because I am very experienced in xleap. You may well want to use some
other graphical or non-graphical program to do this.]

> the program is working properly with the sustiva molecule from the
> tutorial...Any idea?

This is because "EFZ" is known to reduce (it is in its library). Maybe you
just need to change "LIG" to the real name (that used by the PDB), if you know
what it is.


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Received on Fri Mar 20 2015 - 06:00:05 PDT
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