[AMBER] Generating a HETATM database to use with reduce

From: Kucharski Jr., Amir N <amir.kucharski.uky.edu>
Date: Thu, 14 Jul 2016 04:01:37 +0000

Hi all,

I am trying to do simulations on several protein-ligand complexes. I know from the SUS tutorial that reducing the ligand to add hydrogens is a key early step, but these ligands do not have entries in the database that reduce uses. To remedy this, we have tried making our own database from connectivity information in the mol2 files. We have followed the input format for the default library, but when we direct reduce to our database using the -DB tag, still no hydrogens are added. Is there another file we would need to make? Any help is much appreciated. Thanks!

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Received on Wed Jul 13 2016 - 21:30:02 PDT
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