Re: [AMBER] adding missing ligand records to $AMBERHOME/dat/reduce_wwPDB_het_dict.txt

From: David A Case <>
Date: Sat, 2 Jul 2016 07:58:41 -0400

On Sat, Jul 02, 2016, Jose Manuel wrote:
> Actually, I found a script directly within the AmberTools directory that
> did the trick for me:
> $AMBERHOME/AmberTools/src/reduce/

Neat...I didn't know about this file. We can update the dictionary that
we distribute. Thanks for the tip.

Be aware, however, that PDB monomers are generally defined to be neutral,
which is often not what one wants. For example, acetic acid (ACY) has
a protonated carboxylate, which would only be appropriate at very low pH.
I program with more chemical "smarts" than reduce is generally required
if you want automated hydrogen addition.

On the other hand, if you are just doing this occasionally, reduce can be a
big help...just be sure to manually add or remove hydrogens from common acidic
or basic groups.


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Received on Sat Jul 02 2016 - 05:00:04 PDT
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